diff --git a/MediaBrowser.Api/HttpHandlers/AudioHandler.cs b/MediaBrowser.Api/HttpHandlers/AudioHandler.cs
index 294a5b7afc..51d7ba06ae 100644
--- a/MediaBrowser.Api/HttpHandlers/AudioHandler.cs
+++ b/MediaBrowser.Api/HttpHandlers/AudioHandler.cs
@@ -5,6 +5,7 @@ using System.IO;
 using System.Linq;
 using System.Net;
 using System.Threading.Tasks;
+using MediaBrowser.Common.Configuration;
 using MediaBrowser.Common.Logging;
 using MediaBrowser.Common.Net;
 using MediaBrowser.Common.Net.Handlers;
@@ -241,16 +242,26 @@ namespace MediaBrowser.Api.HttpHandlers
             Process process = new Process();
             process.StartInfo = startInfo;
 
+            // FFMpeg writes debug info to StdErr. This is useful when debugging so let's put it in the log directory.
+            FileStream logStream = new FileStream(Path.Combine(ApplicationPaths.LogDirectoryPath, "ffmpeg-" + Guid.NewGuid().ToString() + ".txt"), FileMode.Create);
+
             try
             {
                 process.Start();
 
                 // MUST read both stdout and stderr asynchronously or a deadlock may occurr
-                process.BeginErrorReadLine();
+                // If we ever decide to disable the ffmpeg log then you must uncomment the below line.
+                //process.BeginErrorReadLine();
+
+                Task errorTask = Task.Run(async () => { await process.StandardError.BaseStream.CopyToAsync(logStream); });
 
                 await process.StandardOutput.BaseStream.CopyToAsync(stream);
 
                 process.WaitForExit();
+
+                await errorTask;
+
+                Logger.LogInfo("FFMpeg exited with code " + process.ExitCode);
             }
             catch (Exception ex)
             {
@@ -258,6 +269,7 @@ namespace MediaBrowser.Api.HttpHandlers
             }
             finally
             {
+                logStream.Dispose();
                 process.Dispose();
             }
         }
diff --git a/MediaBrowser.Api/HttpHandlers/VideoHandler.cs b/MediaBrowser.Api/HttpHandlers/VideoHandler.cs
index 1b5c50c38a..0b556b886a 100644
--- a/MediaBrowser.Api/HttpHandlers/VideoHandler.cs
+++ b/MediaBrowser.Api/HttpHandlers/VideoHandler.cs
@@ -54,6 +54,21 @@ namespace MediaBrowser.Api.HttpHandlers
             return false;
         }
 
+        private string GetFFMpegOutputFormat(string outputFormat)
+        {
+            if (outputFormat.Equals("mkv", StringComparison.OrdinalIgnoreCase))
+            {
+                return "matroska";
+            }
+
+            return outputFormat;
+        }
+
+        private int GetOutputAudioStreamIndex(string outputFormat)
+        {
+            return 0;
+        }
+
         /// <summary>
         /// Creates arguments to pass to ffmpeg
         /// </summary>
@@ -62,8 +77,61 @@ namespace MediaBrowser.Api.HttpHandlers
             List<string> audioTranscodeParams = new List<string>();
 
             string outputFormat = GetOutputFormat();
-            outputFormat = "matroska";
-            return "-i \"" + LibraryItem.Path + "\"  -vcodec copy -acodec copy -f " + outputFormat + " -";
+
+            int audioStreamIndex = GetOutputAudioStreamIndex(outputFormat);
+
+            List<string> maps = new List<string>();
+
+            // Add the video stream
+            maps.Add("-map 0:0");
+
+            // Add the audio stream
+            if (audioStreamIndex != -1)
+            {
+                maps.Add("-map 0:" + (1 + audioStreamIndex));
+            }
+
+            // Add all the subtitle streams
+            for (int i = 0; i < LibraryItem.Subtitles.Count(); i++)
+            {
+                maps.Add("-map 0:" + (1 + LibraryItem.AudioStreams.Count() + i));
+
+            }
+
+            return string.Format("-i \"{0}\" {1} {2} {3} -f {4} -",
+                LibraryItem.Path,
+                string.Join(" ", maps.ToArray()),
+                GetVideoArguments(),
+                GetAudioArguments(),
+                GetFFMpegOutputFormat(outputFormat)
+                );
+        }
+
+        private string GetVideoArguments()
+        {
+            return "-c:v copy";
+        }
+
+        private string GetAudioArguments()
+        {
+            return "-c:a copy";
+        }
+
+        private string GetSubtitleArguments()
+        {
+            string args = "";
+
+            for (int i = 0; i < LibraryItem.Subtitles.Count(); i++)
+            {
+                if (i > 0)
+                {
+                    args += " ";
+                }
+                args += "-c:s copy";
+
+            }
+
+            return args;
         }
     }
 }