diff --git a/.travis.yml b/.travis.yml
index dd1f4947..433ad358 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -28,9 +28,11 @@ before_script:
 - $(exit $(misspell -locale US README.md | wc -l))
 - staticcheck $EXCLUDE_VENDOR_AND_PROTO_DIR
 script:
+- set -e
 - mysql -u root -e "CREATE USER 'nss'@'localhost' IDENTIFIED BY 'password'; GRANT ALL PRIVILEGES ON *.* TO 'nss'@'localhost'; CREATE DATABASE test_nats_streaming;"
 - go test -i $EXCLUDE_VENDOR
 - if [[ "$TRAVIS_GO_VERSION" =~ 1.12 ]]; then ./scripts/cov.sh TRAVIS; else go test -failfast $EXCLUDE_VENDOR; fi
+- set +e
 
 deploy:
   provider: script
diff --git a/server/server_run_test.go b/server/server_run_test.go
index c30fc19e..19f76659 100644
--- a/server/server_run_test.go
+++ b/server/server_run_test.go
@@ -486,20 +486,33 @@ func TestPersistentStoreNoPanicOnShutdown(t *testing.T) {
 	defer s.Shutdown()
 
 	// Start a go routine that keeps sending messages
-	sendQuit := make(chan bool)
+	sendQuit := make(chan bool, 1)
 	wg := &sync.WaitGroup{}
 	wg.Add(1)
+	nc, err := nats.Connect(nats.DefaultURL, nats.NoReconnect())
+	if err != nil {
+		t.Fatalf("Error on connect: %v", err)
+	}
+	defer nc.Close()
+	sc, err := stan.Connect(clusterName, clientName,
+		stan.NatsConn(nc),
+		stan.PubAckWait(250*time.Millisecond))
+	if err != nil {
+		t.Fatalf("Error on connect: %v", err)
+	}
+	defer sc.Close()
 	go func() {
 		defer wg.Done()
-
-		sc, nc := createConnectionWithNatsOpts(t, clientName, nats.NoReconnect())
-		defer sc.Close()
-		defer nc.Close()
-
 		payload := []byte("hello")
 		for {
 			select {
 			case <-sendQuit:
+				// We know that the server is shutdown, so close
+				// the NATS connection first so that STAN does not
+				// try to send the close protocol (which will timeout
+				// with a 2sec by default).
+				nc.Close()
+				sc.Close()
 				return
 			default:
 				sc.PublishAsync("foo", payload, nil)
diff --git a/server/server_test.go b/server/server_test.go
index 0327e30a..28159d84 100644
--- a/server/server_test.go
+++ b/server/server_test.go
@@ -432,6 +432,10 @@ func getTestDefaultOptsForPersistentStore() *Options {
 	case stores.TypeFile:
 		opts.FilestoreDir = defaultDataStore
 		opts.FileStoreOpts.BufferSize = 1024
+		// Go 1.12 on macOS is very slow at doing sync writes...
+		if runtime.GOOS == "darwin" && strings.HasPrefix(runtime.Version(), "go1.12") {
+			opts.FileStoreOpts.DoSync = false
+		}
 	case stores.TypeSQL:
 		opts.SQLStoreOpts.Driver = testSQLDriver
 		opts.SQLStoreOpts.Source = testSQLSource
diff --git a/stores/filestore.go b/stores/filestore.go
index 0e19fcbc..dafd0172 100644
--- a/stores/filestore.go
+++ b/stores/filestore.go
@@ -672,6 +672,7 @@ var (
 	bkgTasksSleepDuration = defaultBkgTasksSleepDuration
 	cacheTTL              = int64(defaultCacheTTL)
 	sliceCloseInterval    = defaultSliceCloseInterval
+	fillGaps              = true
 )
 
 // FileStoreTestSetBackgroundTaskInterval is used by tests to reduce the interval
@@ -2622,7 +2623,7 @@ func (ms *FileMsgStore) Store(m *pb.MsgProto) (uint64, error) {
 	ms.needSync = true
 
 	// Is there a gap in message sequence?
-	if ms.last > 0 && m.Sequence > ms.last+1 {
+	if fillGaps && ms.last > 0 && m.Sequence > ms.last+1 {
 		if err := ms.fillGaps(fslice, m); err != nil {
 			ms.unlockFiles(fslice)
 			return 0, err
@@ -2915,6 +2916,11 @@ func (ms *FileMsgStore) expireMsgs(now, maxAge int64) int64 {
 					// Try again in 5 secs.
 					ms.expiration = now + int64(5*time.Second)
 					return ms.expiration
+				} else if m == nil {
+					ms.log.Warnf("Skip expiration of missing sequence %v for channel %q",
+						ms.first, ms.channelName)
+					ms.skipMissingMsg(slice)
+					continue
 				}
 			}
 		}
@@ -2998,14 +3004,53 @@ func (ms *FileMsgStore) readMsgIndex(slice *fileSlice, seq uint64) (*msgIndex, e
 	// Read the index record and ensure we have what we expect
 	seqInIndexFile, msgIndex, err := ms.readIndex(slice.idxFile.handle)
 	if err != nil {
+		if err == io.EOF {
+			return ms.backtrackIndex(slice, seq, seqInIndexFile, idxFileOffset)
+		}
 		return nil, err
 	}
 	if seqInIndexFile != seq {
-		return nil, fmt.Errorf("wrong sequence, wanted %v got %v", seq, seqInIndexFile)
+		return ms.backtrackIndex(slice, seq, seqInIndexFile, idxFileOffset)
 	}
 	return msgIndex, nil
 }
 
+// Looks for the index record for the given `seq` going backward
+// from the give `offset`. This is invoked when the recovered index
+// at the given offset does not the requested sequence, as the result
+// of gaps in the index file.
+func (ms *FileMsgStore) backtrackIndex(slice *fileSlice, seq, wrongSeq uint64, offset int64) (*msgIndex, error) {
+	for offset -= msgIndexRecSize; offset >= 4; offset -= msgIndexRecSize {
+		if _, err := slice.idxFile.handle.Seek(offset, io.SeekStart); err != nil {
+			break
+		}
+		seqInIndexFile, msgIndex, err := ms.readIndex(slice.idxFile.handle)
+		if err == io.EOF {
+			continue
+		}
+		if err == nil && seqInIndexFile == seq {
+			return msgIndex, nil
+		}
+		if err != nil || seqInIndexFile < seq {
+			break
+		}
+	}
+	// Not found...
+	return nil, nil
+}
+
+// When a message is not found due to unexpected gap (from older
+// store since now we ensure there is no gap), bump the first
+// message sequence and update slice.
+func (ms *FileMsgStore) skipMissingMsg(slice *fileSlice) {
+	ms.first++
+	ms.firstMsg = nil
+	if ms.first > ms.last {
+		ms.lastMsg = nil
+	}
+	slice.firstSeq = ms.first
+}
+
 // removeFirstMsg "removes" the first message of the first slice.
 // If the slice is "empty" the file slice is removed.
 func (ms *FileMsgStore) removeFirstMsg(mindex *msgIndex, lockFile bool) error {
@@ -3024,6 +3069,15 @@ func (ms *FileMsgStore) removeFirstMsg(mindex *msgIndex, lockFile bool) error {
 		if err != nil {
 			return err
 		}
+		// Here we are getting the first sequence from the first
+		// available slice, so ms.first and slice.firstSeq should
+		// be the same, but due to possible gaps, they may not.
+		// Adjust in case.
+		ms.first = slice.firstSeq
+	}
+	if mindex == nil {
+		ms.skipMissingMsg(slice)
+		return nil
 	}
 	// Size of the first message in this slice
 	firstMsgSize := mindex.msgSize
@@ -3274,8 +3328,10 @@ func (ms *FileMsgStore) lookup(seq uint64) (*pb.MsgProto, error) {
 		}
 		if ms.readBufSize > 0 && seq != fslice.lastSeq {
 			msg, err = ms.readAheadMsgs(fslice, seq)
-			ms.unlockFiles(fslice)
-			return msg, err
+			if err == nil {
+				ms.unlockFiles(fslice)
+				return msg, err
+			}
 		}
 		msgIndex, err := ms.readMsgIndex(fslice, seq)
 		if msgIndex != nil {
diff --git a/stores/filestore_msg_test.go b/stores/filestore_msg_test.go
index 6fdc2d84..7d65dc99 100644
--- a/stores/filestore_msg_test.go
+++ b/stores/filestore_msg_test.go
@@ -1799,7 +1799,7 @@ func TestFSNoPanicOnRemoveMsg(t *testing.T) {
 
 	limits := testDefaultStoreLimits
 	limits.MaxMsgs = 5
-	s, err := NewFileStore(l, testFSDefaultDatastore, &limits, BufferSize(0), DoCRC(false))
+	s, err := NewFileStore(l, testFSDefaultDatastore, &limits, BufferSize(0))
 	if err != nil {
 		t.Fatalf("Error creating store: %v", err)
 	}
@@ -1820,7 +1820,7 @@ func TestFSNoPanicOnRemoveMsg(t *testing.T) {
 	if err != nil {
 		t.Fatalf("Error reading file: %v", err)
 	}
-	util.ByteOrder.PutUint64(content[4:], 2)
+	copy(content[4:], []byte("xxx"))
 	if err := ioutil.WriteFile(idxFile.name, content, 0600); err != nil {
 		t.Fatalf("Error writing file: %v", err)
 	}
@@ -2092,3 +2092,148 @@ func TestFSReadMsgRecord(t *testing.T) {
 		t.Fatalf("Expected error about wrong size, got %v", err)
 	}
 }
+
+func TestFSGapsInSequenceWithoutFillAndExpiration(t *testing.T) {
+	opts := testFSGetOptionsForGapsTests()
+	// Add case with smaller slice
+	opts = append(opts, testFSGapsOption{
+		name: "SmallFileSlice",
+		opt:  SliceConfig(3, 0, 0, ""),
+	})
+	for _, o := range opts {
+		t.Run(o.name, func(t *testing.T) {
+			fillGaps = false
+			defer func() { fillGaps = true }()
+
+			cleanupFSDatastore(t)
+			defer cleanupFSDatastore(t)
+
+			s := createDefaultFileStore(t, o.opt)
+			defer s.Close()
+
+			limits := testDefaultStoreLimits
+			limits.MaxMsgs = 6
+			s.SetLimits(&limits)
+
+			c := storeCreateChannel(t, s, "foo")
+			ms := c.Msgs.(*FileMsgStore)
+
+			seqs := []uint64{1, 2, 5, 8, 9, 10}
+			for _, seq := range seqs {
+				storeMsg(t, c, "foo", seq, []byte(fmt.Sprintf("msg%d", seq)))
+			}
+			ms.Flush()
+			ms.Lock()
+			ms.cache.empty()
+			ms.Unlock()
+
+			for _, seq := range seqs {
+				msg, err := ms.Lookup(seq)
+				if err != nil {
+					t.Fatalf("Error on lookup: %v", err)
+				}
+				if msg.Sequence != seq || string(msg.Data) != fmt.Sprintf("msg%d", seq) {
+					t.Fatalf("Unexpected message for seq %v: %v", seq, msg)
+				}
+			}
+
+			notfound := []uint64{3, 6, 7}
+			for _, seq := range notfound {
+				msg, err := ms.Lookup(seq)
+				if err != nil || msg != nil {
+					t.Fatalf("Unexpected result err=%v msg=%v", err, msg)
+				}
+			}
+
+			// Add more messages to force 3 first to be removed,
+			// and in the case of the small slice option, should
+			// cause first slice to be removed.
+			// Add some more gaps..
+			storeMsg(t, c, "foo", 12, []byte("msg12"))
+			storeMsg(t, c, "foo", 14, []byte("msg14"))
+			storeMsg(t, c, "foo", 16, []byte("msg16"))
+
+			first, last := msgStoreFirstAndLastSequence(t, ms)
+			if first != 8 && last != 16 {
+				t.Fatalf("Expected first to be 8 and last to be 16, got %v and %v", first, last)
+			}
+
+			expectFirsSliceToBe := func(t *testing.T, expected int) {
+				ms.Lock()
+				ffseq := ms.firstFSlSeq
+				ms.Unlock()
+				if ffseq != expected {
+					t.Fatalf("First slice expected to be %v, got %v", expected, ffseq)
+				}
+			}
+			if o.name == "SmallFileSlice" {
+				expectFirsSliceToBe(t, 2)
+			} else {
+				expectFirsSliceToBe(t, 1)
+			}
+
+			storeMsg(t, c, "foo", 18, []byte("msg18"))
+			storeMsg(t, c, "foo", 19, []byte("msg19"))
+			storeMsg(t, c, "foo", 20, []byte("msg20"))
+
+			// Force expiration..
+			time.Sleep(50 * time.Millisecond)
+			ms.Lock()
+			ms.expireMsgs(time.Now().UnixNano(), int64(time.Millisecond))
+			ms.Unlock()
+
+			n, b, err := ms.State()
+			if err != nil {
+				t.Fatalf("Error getting state: %v", err)
+			}
+			if n != 0 || b != 0 {
+				t.Fatalf("Unexpected number of msgs: %v bytes: %v", n, b)
+			}
+
+			if o.name == "SmallFileSlice" {
+				expectFirsSliceToBe(t, 4)
+			} else {
+				expectFirsSliceToBe(t, 1)
+			}
+		})
+	}
+}
+
+func TestFSExpirationError(t *testing.T) {
+	cleanupFSDatastore(t)
+	defer cleanupFSDatastore(t)
+
+	s := createDefaultFileStore(t)
+	defer s.Close()
+
+	c := storeCreateChannel(t, s, "foo")
+	ms := c.Msgs.(*FileMsgStore)
+
+	storeMsg(t, c, "foo", 1, []byte("msg"))
+	ms.Flush()
+	ms.Lock()
+	ms.cache.empty()
+	ms.Unlock()
+
+	ms.Lock()
+	idxFile := ms.files[1].idxFile
+	ms.fm.closeLockedOrOpenedFile(idxFile)
+	content, err := ioutil.ReadFile(idxFile.name)
+	if err != nil {
+		t.Fatalf("Error reading file: %v", err)
+	}
+	copy(content[4:], []byte("xxx"))
+	if err := ioutil.WriteFile(idxFile.name, content, 0600); err != nil {
+		t.Fatalf("Error writing file: %v", err)
+	}
+	ms.Unlock()
+
+	time.Sleep(50 * time.Millisecond)
+	ms.Lock()
+	now := time.Now().UnixNano()
+	nextExpiration := ms.expireMsgs(time.Now().UnixNano(), int64(time.Millisecond))
+	ms.Unlock()
+	if nextExpiration < now+int64(4500*time.Millisecond) {
+		t.Fatalf("Expected next expiration to be set to 5secs from now, got %v", time.Duration(nextExpiration))
+	}
+}