diff --git a/Core/GameInstance.cs b/Core/GameInstance.cs
index 2b375748f2..2fd5b6fe7e 100644
--- a/Core/GameInstance.cs
+++ b/Core/GameInstance.cs
@@ -341,7 +341,7 @@ public bool Scan()
                 // The least evil is to walk it once, and filter it ourselves.
                 IEnumerable<string> files = Directory
                     .EnumerateFiles(game.PrimaryModDirectory(this), "*", SearchOption.AllDirectories)
-                    .Where(file => dllRegex.IsMatch(file))
+                    .Where(file => file.EndsWith(".dll", StringComparison.CurrentCultureIgnoreCase))
                     .Select(CKANPathUtils.NormalizePath)
                     .Where(absPath => !game.StockFolders.Any(f =>
                         ToRelativeGameDir(absPath).StartsWith($"{f}/")));
@@ -365,8 +365,6 @@ public bool Scan()
             }
         }
 
-        private static readonly Regex dllRegex = new Regex(@"\.dll$", RegexOptions.IgnoreCase | RegexOptions.Compiled);
-
         #endregion
 
         /// <summary>
diff --git a/Core/ModuleInstaller.cs b/Core/ModuleInstaller.cs
index 1511348796..8258d98d94 100644
--- a/Core/ModuleInstaller.cs
+++ b/Core/ModuleInstaller.cs
@@ -333,6 +333,7 @@ private static void CheckKindInstallationKraken(CkanModule module)
         /// <summary>
         /// Installs the module from the zipfile provided.
         /// Returns a list of files installed.
+        /// Propagates a DllLocationMismatchKraken if the user has a bad manual install.
         /// Propagates a BadMetadataKraken if our install metadata is bad.
         /// Propagates a CancelledActionKraken if the user decides not to overwite unowned files.
         /// Propagates a FileExistsKraken if we were going to overwrite a file.
@@ -348,9 +349,27 @@ private IEnumerable<string> InstallModule(CkanModule module, string zip_filename
                 try
                 {
                     var dll = registry.DllPath(module.identifier);
-                    if (dll != null && !files.Any(f => ksp.ToRelativeGameDir(f.destination) == dll))
+                    if (!string.IsNullOrEmpty(dll))
                     {
-                        throw new DllLocationMismatchKraken(dll, $"DLL for module {module.identifier} found at {dll}, but it's not where CKAN would install it. Aborting to prevent multiple copies of the same mod being installed. To install this module, uninstall it manually and try again.");
+                        // Find where we're installing identifier.optionalversion.dll
+                        // (file name might not be an exact match with manually installed)
+                        var dllFolders = files.Where(f =>
+                                Path.GetFileName(f.destination).StartsWith(module.identifier)
+                                    && f.destination.EndsWith(".dll", StringComparison.CurrentCultureIgnoreCase))
+                            .Select(f => Path.GetDirectoryName(ksp.ToRelativeGameDir(f.destination)))
+                            .ToHashSet();
+                        if (!dllFolders.Contains(Path.GetDirectoryName(dll)))
+                        {
+                            // Manually installed DLL is somewhere else where we're not installing files,
+                            // probable bad install, alert user and abort
+                            throw new DllLocationMismatchKraken(dll, $"DLL for module {module.identifier} found at {dll}, but it's not where CKAN would install it. Aborting to prevent multiple copies of the same mod being installed. To install this module, uninstall it manually and try again.");
+                        }
+                        // Delete the manually installed DLL transaction-style because we believe we'll be replacing it
+                        var toDelete = ksp.ToAbsoluteGameDir(dll);
+                        log.DebugFormat("Deleting manually installed DLL {0}", toDelete);
+                        TxFileManager file_transaction = new TxFileManager();
+                        file_transaction.Snapshot(toDelete);
+                        file_transaction.Delete(toDelete);
                     }
 
                     // Look for overwritable files if session is interactive
@@ -474,14 +493,10 @@ private bool StreamsEqual(Stream s1, Stream s2)
         private void DeleteConflictingFiles(IEnumerable<InstallableFile> files)
         {
             TxFileManager file_transaction = new TxFileManager();
-            using (var transaction = CkanTransaction.CreateTransactionScope())
+            foreach (InstallableFile file in files)
             {
-                foreach (InstallableFile file in files)
-                {
-                    log.DebugFormat("Trying to delete {0}", file.destination);
-                    file_transaction.Delete(file.destination);
-                }
-                transaction.Complete();
+                log.DebugFormat("Trying to delete {0}", file.destination);
+                file_transaction.Delete(file.destination);
             }
         }
 
@@ -585,8 +600,8 @@ internal static void CopyZipEntry(ZipFile zipfile, ZipEntry entry, string fullPa
                 }
 
                 // Snapshot whatever was there before. If there's nothing, this will just
-                // remove our file on rollback. We still need this even thought we won't
-                // overwite files, as it ensures deletiion on rollback.
+                // remove our file on rollback. We still need this even though we won't
+                // overwite files, as it ensures deletion on rollback.
                 file_transaction.Snapshot(fullPath);
 
                 try
diff --git a/Core/Registry/Registry.cs b/Core/Registry/Registry.cs
index 05b7c12e7b..3eb35f8fbe 100644
--- a/Core/Registry/Registry.cs
+++ b/Core/Registry/Registry.cs
@@ -836,9 +836,9 @@ public void RegisterDll(GameInstance ksp, string absolute_path)
 
             // http://xkcd.com/208/
             // This regex works great for things like GameData/Foo/Foo-1.2.dll
-            Match match = Regex.Match(
-                relative_path, @"
-                    ^GameData/            # DLLs only live in GameData
+            Match match = Regex.Match(relative_path,
+                // DLLs only live in the primary mod directory
+                $"^{ksp.game.PrimaryModDirectoryRelative}/" + @"
                     (?:.*/)?              # Intermediate paths (ending with /)
                     (?<modname>[^.]+)     # Our DLL name, up until the first dot.
                     .*\.dll$              # Everything else, ending in dll