diff --git a/CHANGELOG.md b/CHANGELOG.md
index 1b02bedffe..0b7e6bc2a0 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -26,6 +26,7 @@ All notable changes to this project will be documented in this file.
 - [GUI] Fix checkbox sorting (#3297 by: HebaruSan; reviewed: DasSkelett)
 - [GUI] Handle incompatible force-installed dependencies of recommendations (#3305 by: HebaruSan; reviewed: DasSkelett)
 - [Multiple] Don't warn about incompatible DLCs, fix conflict highlighting with DLC installed (#3304 by: HebaruSan; reviewed: DasSkelett)
+- [Multiple] Fixes for GUI and .ckan-installed modules (#3307 by: DasSkelett; reviewed: HebaruSan)
 
 ### Internal
 
diff --git a/ConsoleUI/ConsoleCKAN.cs b/ConsoleUI/ConsoleCKAN.cs
index 0e34799f13..c8d2dbd38c 100644
--- a/ConsoleUI/ConsoleCKAN.cs
+++ b/ConsoleUI/ConsoleCKAN.cs
@@ -16,7 +16,7 @@ public class ConsoleCKAN {
         /// </summary>
         public ConsoleCKAN(GameInstanceManager mgr, string themeName, bool debug)
         {
-            if (ConsoleTheme.Themes.TryGetValue(themeName, out ConsoleTheme theme))
+            if (ConsoleTheme.Themes.TryGetValue(themeName ?? "default", out ConsoleTheme theme))
             {
                 // GameInstanceManager only uses its IUser object to construct game instance objects,
                 // which only use it to inform the user about the creation of the CKAN/ folder.
@@ -40,7 +40,7 @@ public ConsoleCKAN(GameInstanceManager mgr, string themeName, bool debug)
                         }
                     }
                     if (manager.CurrentInstance != null) {
-                        new ModListScreen(manager, debug).Run(theme);
+                        new ModListScreen(manager, debug, theme).Run(theme);
                     }
 
                     new ExitScreen().Run(theme);
diff --git a/ConsoleUI/ModListScreen.cs b/ConsoleUI/ModListScreen.cs
index 96c11a0de8..cbc5555375 100644
--- a/ConsoleUI/ModListScreen.cs
+++ b/ConsoleUI/ModListScreen.cs
@@ -17,7 +17,7 @@ public class ModListScreen : ConsoleScreen {
         /// </summary>
         /// <param name="mgr">Game instance manager object containing the current instance</param>
         /// <param name="dbg">True if debug options should be available, false otherwise</param>
-        public ModListScreen(GameInstanceManager mgr, bool dbg)
+        public ModListScreen(GameInstanceManager mgr, bool dbg, ConsoleTheme _theme)
         {
             debug    = dbg;
             manager  = mgr;
@@ -25,7 +25,7 @@ public ModListScreen(GameInstanceManager mgr, bool dbg)
 
             moduleList = new ConsoleListBox<CkanModule>(
                 1, 4, -1, -2,
-                GetAllMods(),
+                GetAllMods(_theme),
                 new List<ConsoleListBoxColumn<CkanModule>>() {
                     new ConsoleListBoxColumn<CkanModule>() {
                         Header   = "",
@@ -205,7 +205,7 @@ public ModListScreen(GameInstanceManager mgr, bool dbg)
                 }
                 return true;
             });
-            
+
             moduleList.AddTip("F8", "Mark auto-installed",
                 () => moduleList.Selection != null && !moduleList.Selection.IsDLC
                     && (!registry.InstalledModule(moduleList.Selection.identifier)?.AutoInstalled ?? false)
@@ -265,7 +265,7 @@ public ModListScreen(GameInstanceManager mgr, bool dbg)
                 null,
                 new ConsoleMenuOption("Refresh mod list", "F5, Ctrl+R",
                     "Refresh the list of mods",
-                    true, UpdateRegistry),
+                    true, (ConsoleTheme th) => UpdateRegistry(th)),
                 new ConsoleMenuOption("Upgrade all",          "Ctrl+U",
                     "Mark all available updates for installation",
                     true, UpgradeAll, null, null, HasAnyUpgradeable()),
@@ -328,7 +328,7 @@ protected override string CenterHeader()
         private bool ImportDownloads(ConsoleTheme theme)
         {
             DownloadImportDialog.ImportDownloads(theme, manager.CurrentInstance, manager.Cache, plan);
-            RefreshList();
+            RefreshList(theme);
             return true;
         }
 
@@ -393,7 +393,7 @@ private bool ViewSuggestions(ConsoleTheme theme)
                         }
                     }
                     if (needRefresh) {
-                        RefreshList();
+                        RefreshList(theme);
                     }
                 } else {
                     RaiseError("Installed mods have no unsatisfied recommendations or suggestions.");
@@ -414,7 +414,7 @@ private int daysSinceUpdated(string filename)
             return (DateTime.Now - File.GetLastWriteTime(filename)).Days;
         }
 
-        private bool UpdateRegistry(ConsoleTheme theme)
+        private bool UpdateRegistry(ConsoleTheme theme, bool showNewModsPrompt = true)
         {
             ProgressScreen ps = new ProgressScreen("Updating Registry", "Checking for updates");
             LaunchSubScreen(theme, ps, (ConsoleTheme th) => {
@@ -447,11 +447,11 @@ private bool UpdateRegistry(ConsoleTheme theme)
                     }
                 }
             });
-            if (recent.Count > 0 && RaiseYesNoDialog(newModPrompt(recent.Count))) {
+            if (showNewModsPrompt && recent.Count > 0 && RaiseYesNoDialog(newModPrompt(recent.Count))) {
                 searchBox.Clear();
                 moduleList.FilterString = searchBox.Value = "~n";
             }
-            RefreshList();
+            RefreshList(theme);
             return true;
         }
 
@@ -481,7 +481,7 @@ private bool SelectInstall(ConsoleTheme theme)
             if (!prevInst.Equals(manager.CurrentInstance)) {
                 plan.Reset();
                 registry = RegistryManager.Instance(manager.CurrentInstance).registry;
-                RefreshList();
+                RefreshList(theme);
             }
             return true;
         }
@@ -492,17 +492,23 @@ private bool EditAuthTokens(ConsoleTheme theme)
             return true;
         }
 
-        private void RefreshList()
+        private void RefreshList(ConsoleTheme theme)
         {
-            moduleList.SetData(GetAllMods(true));
+            // In the constructor this is called while moduleList is being populated, just do nothing in this case.
+            // ModListScreen -> moduleList = (GetAllMods ...) -> UpdateRegistry -> RefreshList
+            moduleList?.SetData(GetAllMods(theme,true));
         }
 
         private List<CkanModule> allMods = null;
 
-        private List<CkanModule> GetAllMods(bool force = false)
+        private List<CkanModule> GetAllMods(ConsoleTheme theme, bool force = false)
         {
             ScanForMods();
             if (allMods == null || force) {
+                if (!registry?.HasAnyAvailable() ?? false)
+                {
+                    UpdateRegistry(theme, false);
+                }
                 allMods = new List<CkanModule>(registry.CompatibleModules(manager.CurrentInstance.VersionCriteria()));
                 foreach (InstalledModule im in registry.InstalledModules) {
                     CkanModule m = null;
@@ -546,7 +552,7 @@ private bool Help(ConsoleTheme theme)
         private bool ApplyChanges(ConsoleTheme theme)
         {
             LaunchSubScreen(theme, new InstallScreen(manager, plan, debug));
-            RefreshList();
+            RefreshList(theme);
             return true;
         }
 
@@ -598,9 +604,9 @@ private long totalInstalledDownloadSize()
             return total;
         }
 
-        private GameInstanceManager       manager;
-        private IRegistryQuerier registry;
-        private bool             debug;
+        private GameInstanceManager manager;
+        private Registry            registry;
+        private bool                debug;
 
         private ConsoleField               searchBox;
         private ConsoleListBox<CkanModule> moduleList;
@@ -839,7 +845,7 @@ public enum InstallStatus {
         /// This mod is installed and not upgradeable or planned to be removed
         /// </summary>
         Installed,
-        
+
         /// <summary>
         /// Like Installed, but can be auto-removed if depending mods are removed
         /// </summary>
diff --git a/Core/ModuleInstaller.cs b/Core/ModuleInstaller.cs
index 3c016494a9..e3d4009ff2 100644
--- a/Core/ModuleInstaller.cs
+++ b/Core/ModuleInstaller.cs
@@ -1347,7 +1347,7 @@ IRegistryQuerier            registry
             {
                 RelationshipResolver resolver = new RelationshipResolver(
                     toInstall,
-                    null,
+                    toInstall.Select(m => registry.InstalledModule(m.identifier)?.Module).Where(m => m != null),
                     opts, registry, ksp.VersionCriteria()
                 );
 
diff --git a/Core/Net/NetAsyncDownloader.cs b/Core/Net/NetAsyncDownloader.cs
index c31794bd45..f2367edd40 100644
--- a/Core/Net/NetAsyncDownloader.cs
+++ b/Core/Net/NetAsyncDownloader.cs
@@ -356,6 +356,8 @@ private void FileProgressReport(int index, int percent, long bytesDownloaded, lo
 
             foreach (NetAsyncDownloaderDownloadPart t in downloads.ToList())
             {
+                if (t == null)
+                    continue;
                 if (t.bytesLeft > 0)
                 {
                     totalBytesPerSecond += t.bytesPerSecond;
@@ -366,6 +368,9 @@ private void FileProgressReport(int index, int percent, long bytesDownloaded, lo
             }
             foreach (Net.DownloadTarget t in queuedDownloads.ToList())
             {
+                // Somehow managed to get a NullRef for t here
+                if (t == null)
+                    continue;
                 totalBytesLeft += t.size;
                 totalSize += t.size;
             }
diff --git a/Core/Registry/IRegistryQuerier.cs b/Core/Registry/IRegistryQuerier.cs
index 1a4e6e87bb..46b272e0f1 100644
--- a/Core/Registry/IRegistryQuerier.cs
+++ b/Core/Registry/IRegistryQuerier.cs
@@ -194,7 +194,7 @@ public static bool HasUpdate(this IRegistryQuerier querier, string identifier, G
             {
                 RelationshipResolver resolver = new RelationshipResolver(
                     new CkanModule[] { newest_version },
-                    null,
+                    new CkanModule[] { querier.InstalledModule(identifier).Module },
                     new RelationshipResolverOptions()
                     {
                         with_recommends = false,
diff --git a/Core/Relationships/RelationshipResolver.cs b/Core/Relationships/RelationshipResolver.cs
index 87fd39ddca..9b45e04ee9 100644
--- a/Core/Relationships/RelationshipResolver.cs
+++ b/Core/Relationships/RelationshipResolver.cs
@@ -247,9 +247,9 @@ private void AddModulesToInstall(IEnumerable<CkanModule> modules)
             {
                 log.DebugFormat("Preparing to resolve relationships for {0} {1}", module.identifier, module.version);
 
-                //Need to check against installed mods and those to install.
-                var mods = modlist.Values.Concat(installed_modules).Where(listed_mod => listed_mod.ConflictsWith(module));
-                foreach (CkanModule listed_mod in mods)
+                // Need to check against installed mods and those to install.
+                var conflictingModules = modlist.Values.Concat(installed_modules).Where(listed_mod => listed_mod.ConflictsWith(module));
+                foreach (CkanModule listed_mod in conflictingModules)
                 {
                     if (options.proceed_with_inconsistencies)
                     {
diff --git a/GUI/Controls/AllModVersions.cs b/GUI/Controls/AllModVersions.cs
index 2641c598a9..5586ca737a 100644
--- a/GUI/Controls/AllModVersions.cs
+++ b/GUI/Controls/AllModVersions.cs
@@ -122,6 +122,11 @@ public GUIMod SelectedModule
                         visibleGuiModule.PropertyChanged += visibleGuiModule_PropertyChanged;
                     }
                 }
+                VersionsListView.Items.Clear();
+                if (value == null)
+                {
+                    return;
+                }
 
                 // Get all the data; can put this in bg if slow
                 GameInstance currentInstance = Main.Instance.Manager.CurrentInstance;
@@ -139,16 +144,28 @@ public GUIMod SelectedModule
                 }
                 catch (ModuleNotFoundKraken)
                 {
-                    // No versions to be shown, abort and hope an auto refresh happens
+                    // Identifier unknown to registry, maybe installed from local .ckan
+                    allAvailableVersions = new Dictionary<CkanModule, bool>();
+                }
+
+                // Take the module associated with GUIMod, if any, and append it to the list if it's not already there.
+                var installedModule = value.InstalledMod?.Module;
+                if (installedModule != null && !allAvailableVersions.ContainsKey(installedModule))
+                {
+                    allAvailableVersions.Add(installedModule, installable(installer, installedModule, registry));
+                }
+
+                if (!allAvailableVersions.Any())
+                {
                     return;
                 }
+
                 ModuleVersion installedVersion = registry.InstalledVersion(value.Identifier);
 
                 // Update UI; must be in fg
                 ignoreItemCheck = true;
                 bool latestCompatibleVersionAlreadyFound = false;
 
-                VersionsListView.Items.Clear();
                 // Only show checkboxes for non-DLC modules
                 VersionsListView.CheckBoxes = !value.ToModule().IsDLC;
 
diff --git a/GUI/Controls/ManageMods.Designer.cs b/GUI/Controls/ManageMods.Designer.cs
index 1e4ac0a7b5..294b8e574e 100644
--- a/GUI/Controls/ManageMods.Designer.cs
+++ b/GUI/Controls/ManageMods.Designer.cs
@@ -1,4 +1,6 @@
-namespace CKAN
+using System.Windows.Forms;
+
+namespace CKAN
 {
     partial class ManageMods
     {
@@ -98,6 +100,7 @@ private void InitializeComponent()
             this.FilterToolButton,
             this.NavBackwardToolButton,
             this.NavForwardToolButton});
+            this.menuStrip2.CanOverflow = true;
             this.menuStrip2.Location = new System.Drawing.Point(0, 0);
             this.menuStrip2.Name = "menuStrip2";
             this.menuStrip2.Size = new System.Drawing.Size(5876, 48);
@@ -110,6 +113,7 @@ private void InitializeComponent()
             this.launchGameToolStripMenuItem.ImageScaling = System.Windows.Forms.ToolStripItemImageScaling.None;
             this.launchGameToolStripMenuItem.Name = "launchGameToolStripMenuItem";
             this.launchGameToolStripMenuItem.Size = new System.Drawing.Size(146, 56);
+            this.launchGameToolStripMenuItem.Overflow = ToolStripItemOverflow.AsNeeded;
             this.launchGameToolStripMenuItem.Click += new System.EventHandler(this.launchGameToolStripMenuItem_Click);
             resources.ApplyResources(this.launchGameToolStripMenuItem, "launchGameToolStripMenuItem");
             //
@@ -119,6 +123,7 @@ private void InitializeComponent()
             this.RefreshToolButton.ImageScaling = System.Windows.Forms.ToolStripItemImageScaling.None;
             this.RefreshToolButton.Name = "RefreshToolButton";
             this.RefreshToolButton.Size = new System.Drawing.Size(114, 56);
+            this.RefreshToolButton.Overflow = ToolStripItemOverflow.AsNeeded;
             this.RefreshToolButton.Click += new System.EventHandler(this.RefreshToolButton_Click);
             resources.ApplyResources(this.RefreshToolButton, "RefreshToolButton");
             //
@@ -128,6 +133,7 @@ private void InitializeComponent()
             this.UpdateAllToolButton.ImageScaling = System.Windows.Forms.ToolStripItemImageScaling.None;
             this.UpdateAllToolButton.Name = "UpdateAllToolButton";
             this.UpdateAllToolButton.Size = new System.Drawing.Size(232, 56);
+            this.UpdateAllToolButton.Overflow = ToolStripItemOverflow.AsNeeded;
             this.UpdateAllToolButton.Click += new System.EventHandler(this.MarkAllUpdatesToolButton_Click);
             resources.ApplyResources(this.UpdateAllToolButton, "UpdateAllToolButton");
             //
@@ -137,6 +143,7 @@ private void InitializeComponent()
             this.ApplyToolButton.ImageScaling = System.Windows.Forms.ToolStripItemImageScaling.None;
             this.ApplyToolButton.Name = "ApplyToolButton";
             this.ApplyToolButton.Size = new System.Drawing.Size(173, 56);
+            this.ApplyToolButton.Overflow = ToolStripItemOverflow.AsNeeded;
             this.ApplyToolButton.Click += new System.EventHandler(this.ApplyToolButton_Click);
             resources.ApplyResources(this.ApplyToolButton, "ApplyToolButton");
             //
@@ -161,6 +168,7 @@ private void InitializeComponent()
             this.FilterToolButton.ImageScaling = System.Windows.Forms.ToolStripItemImageScaling.None;
             this.FilterToolButton.Name = "FilterToolButton";
             this.FilterToolButton.Size = new System.Drawing.Size(201, 56);
+            this.FilterToolButton.Overflow = ToolStripItemOverflow.AsNeeded;
             resources.ApplyResources(this.FilterToolButton, "FilterToolButton");
             //
             // FilterCompatibleButton
@@ -253,6 +261,7 @@ private void InitializeComponent()
             this.NavBackwardToolButton.ImageScaling = System.Windows.Forms.ToolStripItemImageScaling.None;
             this.NavBackwardToolButton.Name = "NavBackwardToolButton";
             this.NavBackwardToolButton.Size = new System.Drawing.Size(44, 56);
+            this.NavBackwardToolButton.Overflow = ToolStripItemOverflow.AsNeeded;
             this.NavBackwardToolButton.Click += new System.EventHandler(this.NavBackwardToolButton_Click);
             resources.ApplyResources(this.NavBackwardToolButton, "NavBackwardToolButton");
             //
@@ -262,6 +271,7 @@ private void InitializeComponent()
             this.NavForwardToolButton.ImageScaling = System.Windows.Forms.ToolStripItemImageScaling.None;
             this.NavForwardToolButton.Name = "NavForwardToolButton";
             this.NavForwardToolButton.Size = new System.Drawing.Size(44, 56);
+            this.NavForwardToolButton.Overflow = ToolStripItemOverflow.AsNeeded;
             this.NavForwardToolButton.Click += new System.EventHandler(this.NavForwardToolButton_Click);
             resources.ApplyResources(this.NavForwardToolButton, "NavForwardToolButton");
             //
diff --git a/GUI/Controls/ManageMods.cs b/GUI/Controls/ManageMods.cs
index 76eb2492a1..36106baa26 100644
--- a/GUI/Controls/ManageMods.cs
+++ b/GUI/Controls/ManageMods.cs
@@ -786,8 +786,21 @@ public void ClearChangeSet()
                 {
                     mod.SetInstallChecked(row, Installed, mod.IsInstalled);
                 }
+                else if (mod.SelectedMod != mod.InstalledMod?.Module)
+                {
+                    mod.SelectedMod = mod.InstalledMod?.Module;
+                }
                 mod.SetUpgradeChecked(row, UpdateCol, false);
                 mod.SetReplaceChecked(row, ReplaceCol, false);
+                // Marking a mod as AutoInstalled can immediately queue it for removal if there is no dependent mod.
+                // Reset the state of the AutoInstalled checkbox for these by deducing it from the changeset.
+                if (mod.InstalledMod != null &&
+                    ChangeSet.Contains(new ModChange(mod.InstalledMod?.Module, GUIModChangeType.Remove,
+                        new SelectionReason.NoLongerUsed()))
+                )
+                {
+                    mod.SetAutoInstallChecked(row, AutoInstalled, false);
+                }
             }
         }
 
diff --git a/GUI/Controls/ModInfo.cs b/GUI/Controls/ModInfo.cs
index 714eeeb3fb..5084358d43 100644
--- a/GUI/Controls/ModInfo.cs
+++ b/GUI/Controls/ModInfo.cs
@@ -140,7 +140,7 @@ private void UpdateModInfo(GUIMod gui_module)
             Util.Invoke(MetadataModuleAuthorTextBox, () => MetadataModuleAuthorTextBox.Text = gui_module.Authors);
             Util.Invoke(MetadataIdentifierTextBox, () => MetadataIdentifierTextBox.Text = module.identifier);
 
-            Util.Invoke(MetadataModuleReleaseStatusTextBox, () => 
+            Util.Invoke(MetadataModuleReleaseStatusTextBox, () =>
             {
                 if (module.release_status == null)
                 {
diff --git a/GUI/Controls/Wait.Designer.cs b/GUI/Controls/Wait.Designer.cs
index 51b994eca0..8f6715cb71 100644
--- a/GUI/Controls/Wait.Designer.cs
+++ b/GUI/Controls/Wait.Designer.cs
@@ -37,18 +37,19 @@ private void InitializeComponent()
             this.BottomButtonPanel = new System.Windows.Forms.Panel();
             this.CancelCurrentActionButton = new System.Windows.Forms.Button();
             this.RetryCurrentActionButton = new System.Windows.Forms.Button();
+            this.OkButton = new System.Windows.Forms.Button();
             this.SuspendLayout();
-            // 
+            //
             // TopPanel
-            // 
+            //
             this.TopPanel.Controls.Add(this.MessageTextBox);
             this.TopPanel.Controls.Add(this.DialogProgressBar);
             this.TopPanel.Dock = System.Windows.Forms.DockStyle.Top;
             this.TopPanel.Name = "TopPanel";
             this.TopPanel.Size = new System.Drawing.Size(500, 85);
-            // 
+            //
             // MessageTextBox
-            // 
+            //
             this.MessageTextBox.Anchor = ((System.Windows.Forms.AnchorStyles)(((System.Windows.Forms.AnchorStyles.Top | System.Windows.Forms.AnchorStyles.Left)
             | System.Windows.Forms.AnchorStyles.Right)));            this.MessageTextBox.BackColor = System.Drawing.SystemColors.Control;
             this.MessageTextBox.BorderStyle = System.Windows.Forms.BorderStyle.None;
@@ -62,9 +63,9 @@ private void InitializeComponent()
             this.MessageTextBox.TabIndex = 0;
             this.MessageTextBox.TextAlign = System.Windows.Forms.HorizontalAlignment.Center;
             resources.ApplyResources(this.MessageTextBox, "MessageTextBox");
-            // 
+            //
             // DialogProgressBar
-            // 
+            //
             this.DialogProgressBar.Anchor = ((System.Windows.Forms.AnchorStyles)(((System.Windows.Forms.AnchorStyles.Top | System.Windows.Forms.AnchorStyles.Left)
             | System.Windows.Forms.AnchorStyles.Right)));
             this.DialogProgressBar.Location = new System.Drawing.Point(5, 45);
@@ -75,9 +76,9 @@ private void InitializeComponent()
             this.DialogProgressBar.Size = new System.Drawing.Size(490, 25);
             this.DialogProgressBar.Style = System.Windows.Forms.ProgressBarStyle.Marquee;
             this.DialogProgressBar.TabIndex = 1;
-            // 
+            //
             // LogTextBox
-            // 
+            //
             this.LogTextBox.Dock = System.Windows.Forms.DockStyle.Fill;
             this.LogTextBox.BorderStyle = System.Windows.Forms.BorderStyle.FixedSingle;
             this.LogTextBox.Location = new System.Drawing.Point(14, 89);
@@ -89,41 +90,54 @@ private void InitializeComponent()
             this.LogTextBox.ScrollBars = System.Windows.Forms.ScrollBars.Vertical;
             this.LogTextBox.Size = new System.Drawing.Size(500, 400);
             this.LogTextBox.TabIndex = 2;
-            // 
+            //
             // BottomButtonPanel
-            // 
-            this.BottomButtonPanel.Controls.Add(this.CancelCurrentActionButton);
+            //
             this.BottomButtonPanel.Controls.Add(this.RetryCurrentActionButton);
+            this.BottomButtonPanel.Controls.Add(this.CancelCurrentActionButton);
+            this.BottomButtonPanel.Controls.Add(this.OkButton);
             this.BottomButtonPanel.Dock = System.Windows.Forms.DockStyle.Bottom;
             this.BottomButtonPanel.Name = "BottomButtonPanel";
             this.BottomButtonPanel.Size = new System.Drawing.Size(500, 40);
-            // 
+            //
             // RetryCurrentActionButton
-            // 
+            //
             this.RetryCurrentActionButton.Anchor = ((System.Windows.Forms.AnchorStyles)((System.Windows.Forms.AnchorStyles.Bottom | System.Windows.Forms.AnchorStyles.Right)));
             this.RetryCurrentActionButton.FlatStyle = System.Windows.Forms.FlatStyle.Flat;
-            this.RetryCurrentActionButton.Location = new System.Drawing.Point(266, 5);
+            this.RetryCurrentActionButton.Location = new System.Drawing.Point(149, 5);
             this.RetryCurrentActionButton.Margin = new System.Windows.Forms.Padding(4, 5, 4, 5);
             this.RetryCurrentActionButton.Name = "RetryCurrentActionButton";
             this.RetryCurrentActionButton.Size = new System.Drawing.Size(112, 30);
             this.RetryCurrentActionButton.TabIndex = 3;
             this.RetryCurrentActionButton.Click += new System.EventHandler(this.RetryCurrentActionButton_Click);
             resources.ApplyResources(this.RetryCurrentActionButton, "RetryCurrentActionButton");
-            // 
+            //
             // CancelCurrentActionButton
-            // 
+            //
             this.CancelCurrentActionButton.Anchor = ((System.Windows.Forms.AnchorStyles)((System.Windows.Forms.AnchorStyles.Bottom | System.Windows.Forms.AnchorStyles.Right)));
             this.CancelCurrentActionButton.FlatStyle = System.Windows.Forms.FlatStyle.Flat;
-            this.CancelCurrentActionButton.Location = new System.Drawing.Point(383, 5);
+            this.CancelCurrentActionButton.Location = new System.Drawing.Point(266, 5);
             this.CancelCurrentActionButton.Margin = new System.Windows.Forms.Padding(4, 5, 4, 5);
             this.CancelCurrentActionButton.Name = "CancelCurrentActionButton";
             this.CancelCurrentActionButton.Size = new System.Drawing.Size(112, 30);
             this.CancelCurrentActionButton.TabIndex = 4;
             this.CancelCurrentActionButton.Click += new System.EventHandler(this.CancelCurrentActionButton_Click);
             resources.ApplyResources(this.CancelCurrentActionButton, "CancelCurrentActionButton");
-            // 
+            //
+            // OkButton
+            //
+            this.OkButton.Anchor = ((System.Windows.Forms.AnchorStyles)((System.Windows.Forms.AnchorStyles.Bottom | System.Windows.Forms.AnchorStyles.Right)));
+            this.OkButton.FlatStyle = System.Windows.Forms.FlatStyle.Flat;
+            this.OkButton.Location = new System.Drawing.Point(383, 5);
+            this.OkButton.Margin = new System.Windows.Forms.Padding(4, 5, 4, 5);
+            this.OkButton.Name = "OkButton";
+            this.OkButton.Size = new System.Drawing.Size(112, 30);
+            this.OkButton.TabIndex = 5;
+            this.OkButton.Click += new System.EventHandler(this.OkButton_Click);
+            resources.ApplyResources(this.OkButton, "OkButton");
+            //
             // Wait
-            // 
+            //
             this.AutoScaleMode = System.Windows.Forms.AutoScaleMode.None;
             this.Controls.Add(this.LogTextBox);
             this.Controls.Add(this.TopPanel);
@@ -146,5 +160,6 @@ private void InitializeComponent()
         private System.Windows.Forms.Panel BottomButtonPanel;
         private System.Windows.Forms.Button RetryCurrentActionButton;
         private System.Windows.Forms.Button CancelCurrentActionButton;
+        private System.Windows.Forms.Button OkButton;
     }
 }
diff --git a/GUI/Controls/Wait.cs b/GUI/Controls/Wait.cs
index b2016bfb2a..36bda98f82 100644
--- a/GUI/Controls/Wait.cs
+++ b/GUI/Controls/Wait.cs
@@ -17,6 +17,7 @@ public Wait()
 
         public event Action OnRetry;
         public event Action OnCancel;
+        public event Action OnOk;
 
         public bool RetryEnabled
         {
@@ -199,6 +200,7 @@ public void Reset(bool cancelable)
                 ProgressIndeterminate = true;
                 RetryCurrentActionButton.Enabled = false;
                 CancelCurrentActionButton.Enabled = cancelable;
+                OkButton.Enabled = false;
                 MessageTextBox.Text = Properties.Resources.MainWaitPleaseWait;
             });
         }
@@ -212,6 +214,7 @@ public void Finish(bool success)
                 ProgressIndeterminate = false;
                 RetryCurrentActionButton.Enabled = !success;
                 CancelCurrentActionButton.Enabled = false;
+                OkButton.Enabled = true;
             });
         }
 
@@ -250,5 +253,13 @@ private void CancelCurrentActionButton_Click(object sender, EventArgs e)
             Util.Invoke(this, () =>
                 CancelCurrentActionButton.Enabled = false);
         }
+
+        private void OkButton_Click(object sender, EventArgs e)
+        {
+            if (OnOk != null)
+            {
+                OnOk();
+            }
+        }
     }
 }
diff --git a/GUI/Controls/Wait.resx b/GUI/Controls/Wait.resx
index 4ac4273fb8..e273d4364b 100644
--- a/GUI/Controls/Wait.resx
+++ b/GUI/Controls/Wait.resx
@@ -119,5 +119,6 @@
   </resheader>
   <data name="CancelCurrentActionButton.Text" xml:space="preserve"><value>Cancel</value></data>
   <data name="RetryCurrentActionButton.Text" xml:space="preserve"><value>Retry</value></data>
+  <data name="OkButton.Text" xml:space="preserve"><value>OK</value></data>
   <data name="MessageTextBox.Text" xml:space="preserve"><value>Waiting for operation to complete</value></data>
 </root>
diff --git a/GUI/Dialogs/ManageGameInstancesDialog.cs b/GUI/Dialogs/ManageGameInstancesDialog.cs
index 2158b625d7..4a04afafb0 100644
--- a/GUI/Dialogs/ManageGameInstancesDialog.cs
+++ b/GUI/Dialogs/ManageGameInstancesDialog.cs
@@ -19,7 +19,7 @@ public partial class ManageGameInstancesDialog : Form
             Filter           = GameFolderFilter(Main.Instance.Manager),
             Multiselect      = false
         };
-        
+
         /// <summary>
         /// Generate filter string for OpenFileDialog
         /// </summary>
@@ -213,7 +213,7 @@ private void GameInstancesListView_Click(object sender, MouseEventArgs e)
 
         private void OpenDirectoryMenuItem_Click(object sender, EventArgs e)
         {
-            string path = GameInstancesListView.SelectedItems[0].SubItems[2].Text;
+            string path = _manager.Instances[(string) GameInstancesListView.SelectedItems[0].Tag].GameDir();
 
             if (!Directory.Exists(path))
             {
diff --git a/GUI/Main/Main.Designer.cs b/GUI/Main/Main.Designer.cs
index 2fb74ff161..17e51b02fe 100644
--- a/GUI/Main/Main.Designer.cs
+++ b/GUI/Main/Main.Designer.cs
@@ -401,9 +401,9 @@ private void InitializeComponent()
             this.ManageModsTabPage.Size = new System.Drawing.Size(1536, 948);
             this.ManageModsTabPage.TabIndex = 3;
             resources.ApplyResources(this.ManageModsTabPage, "ManageModsTabPage");
-            // 
+            //
             // ManageMods
-            // 
+            //
             this.ManageMods.Dock = System.Windows.Forms.DockStyle.Fill;
             this.ManageMods.Location = new System.Drawing.Point(0, 0);
             this.ManageMods.Margin = new System.Windows.Forms.Padding(0,0,0,0);
@@ -467,6 +467,7 @@ private void InitializeComponent()
             this.Wait.TabIndex = 32;
             this.Wait.OnRetry += Wait_OnRetry;
             this.Wait.OnCancel += Wait_OnCancel;
+            this.Wait.OnOk += Wait_OnOk;
             //
             // ChooseRecommendedModsTabPage
             //
diff --git a/GUI/Main/MainChangeset.cs b/GUI/Main/MainChangeset.cs
index db2935f90c..51d59d51cd 100644
--- a/GUI/Main/MainChangeset.cs
+++ b/GUI/Main/MainChangeset.cs
@@ -1,3 +1,4 @@
+using System;
 using System.Linq;
 using System.Collections.Generic;
 using System.Windows.Forms;
@@ -37,13 +38,22 @@ private void Changeset_OnConfirmChanges()
             // Using the changeset passed in can cause issues with versions.
             // An example is Mechjeb for FAR at 25/06/2015 with a 1.0.2 install.
             // TODO Work out why this is.
-            installWorker.RunWorkerAsync(
-                new KeyValuePair<List<ModChange>, RelationshipResolverOptions>(
-                    ManageMods.mainModList.ComputeUserChangeSet(RegistryManager.Instance(Main.Instance.CurrentInstance).registry).ToList(),
-                    RelationshipResolver.DependsOnlyOpts()
-                )
-            );
+            try
+            {
+                installWorker.RunWorkerAsync(
+                    new KeyValuePair<List<ModChange>, RelationshipResolverOptions>(
+                        ManageMods.mainModList
+                            .ComputeUserChangeSet(RegistryManager.Instance(Main.Instance.CurrentInstance).registry)
+                            .ToList(),
+                        RelationshipResolver.DependsOnlyOpts()
+                    )
+                );
+            }
+            catch (InvalidOperationException)
+            {
+                // Thrown if it's already busy, can happen if the user fouble-clicks the button. Ignore it.
+                // More thread-safe than checking installWorker.IsBusy beforehand.
+            }
         }
-
     }
 }
diff --git a/GUI/Main/MainInstall.cs b/GUI/Main/MainInstall.cs
index e879dd83d4..09ed64db22 100644
--- a/GUI/Main/MainInstall.cs
+++ b/GUI/Main/MainInstall.cs
@@ -142,6 +142,8 @@ out Dictionary<CkanModule, HashSet<string>> supporters
 
             if (installCanceled)
             {
+                Util.Invoke(this, () => Enabled = true);
+                Util.Invoke(menuStrip1, () => menuStrip1.Enabled = true);
                 tabController.ShowTab("ManageModsTabPage");
                 e.Result = new KeyValuePair<bool, ModChanges>(false, opts.Key);
                 return;
@@ -236,6 +238,8 @@ out Dictionary<CkanModule, HashSet<string>> supporters
                     {
                         // User cancelled, get out
                         tabController.ShowTab("ManageModsTabPage");
+                        Util.Invoke(this, () => Enabled = true);
+                        Util.Invoke(menuStrip1, () => menuStrip1.Enabled = true);
                         e.Result = new KeyValuePair<bool, ModChanges>(false, opts.Key);
                         return;
                     }
@@ -291,7 +295,11 @@ private void OnModInstalled(CkanModule mod)
 
         private void PostInstallMods(object sender, RunWorkerCompletedEventArgs e)
         {
-            tabController.SetTabLock(false);
+            okCallback = () =>
+            {
+                ManageMods.UpdateModsList(null);
+                okCallback = null;
+            };
 
             if (e.Error != null)
             {
@@ -410,7 +418,10 @@ private void PostInstallMods(object sender, RunWorkerCompletedEventArgs e)
                         }
                     }
 
-                    // install successful
+                    Util.Invoke(this, () => Enabled = true);
+                    Util.Invoke(menuStrip1, () => menuStrip1.Enabled = true);
+                    tabController.SetTabLock(false);
+
                     AddStatusMessage(Properties.Resources.MainInstallSuccess);
                     HideWaitDialog(true);
                 }
@@ -434,9 +445,6 @@ private void PostInstallMods(object sender, RunWorkerCompletedEventArgs e)
                     }
                 }
             }
-
-            Util.Invoke(this, () => Enabled = true);
-            Util.Invoke(menuStrip1, () => menuStrip1.Enabled = true);
         }
     }
 }
diff --git a/GUI/Main/MainWait.cs b/GUI/Main/MainWait.cs
index eb23a69c19..bddfaf3334 100644
--- a/GUI/Main/MainWait.cs
+++ b/GUI/Main/MainWait.cs
@@ -6,6 +6,7 @@ namespace CKAN
     public partial class Main
     {
         private Action cancelCallback;
+        private Action okCallback;
 
         public void ShowWaitDialog(bool cancelable = true)
         {
@@ -87,5 +88,16 @@ public void Wait_OnCancel()
                 cancelCallback();
             }
         }
+
+        public void Wait_OnOk()
+        {
+            if (okCallback != null)
+            {
+                okCallback();
+            }
+            Util.Invoke(this, () => Enabled = true);
+            Util.Invoke(menuStrip1, () => menuStrip1.Enabled = true);
+            tabController.SetTabLock(false);
+        }
     }
 }
diff --git a/GUI/Model/GUIMod.cs b/GUI/Model/GUIMod.cs
index b45152d09d..6737390908 100644
--- a/GUI/Model/GUIMod.cs
+++ b/GUI/Model/GUIMod.cs
@@ -12,7 +12,7 @@ public sealed class GUIMod : INotifyPropertyChanged
     {
         private CkanModule      Mod                 { get; set; }
         private CkanModule      LatestCompatibleMod { get; set; }
-        private InstalledModule InstalledMod        { get; set; }
+        public  InstalledModule InstalledMod        { get; private set; }
 
         /// <summary>
         /// The module of the checkbox that is checked in the MainAllModVersions list if any,
@@ -141,6 +141,8 @@ public GUIMod(InstalledModule instMod, IRegistryQuerier registry, GameVersionCri
             {
                 LatestVersion = InstalledVersion;
             }
+            // For mods not known to the registry LatestCompatibleMod is null, however the installed module might be compatible
+            IsIncompatible   = incompatible ?? LatestCompatibleMod == null && !instMod.Module.IsCompatibleKSP(current_game_version);
         }
 
         /// <summary>
@@ -268,6 +270,12 @@ public void UpdateIsCached()
             IsCached = Main.Instance.Manager.Cache.IsMaybeCachedZip(Mod);
         }
 
+        /// <summary>
+        /// Get the CkanModule associated with this GUIMod.
+        /// See <see cref="ToModule"/> for a method that doesn't throw.
+        /// </summary>
+        /// <returns>The CkanModule associated with this GUIMod</returns>
+        /// <exception cref="InvalidCastException">Thrown if no CkanModule is associated</exception>
         public CkanModule ToCkanModule()
         {
             if (!IsCKAN)
@@ -276,6 +284,10 @@ public CkanModule ToCkanModule()
             return mod;
         }
 
+        /// <summary>
+        /// Get the CkanModule associated with this GUIMod.
+        /// </summary>
+        /// <returns>The CkanModule associated with this GUIMod or null if there is none</returns>
         public CkanModule ToModule()
         {
             return Mod;