This is how I do it.
This is how I do it.
Workaround...
[1] Acquire BOTH the MKV and the AVI versions of the file.
[2] Strip audio from the AVI version save as AAC (or whatever you fancy)
[3] Pull MKV into MKVTOOLNIX
[4] Pull new MP4 audio file into MKVTOOLNIX
[5] Un tick the original audio source in toolnix (so it will not be muxed) - set both the video and new audio source to 'none' compression in extra options tab and remux
[6]Now parse the new file through MKV2VOB - AAC will be converted to AC3
[7] All Done - will now play fine - as the groups audio files should be the same no sync issues should be apparent.
As the avi version have exactly the same problem with the audio stream as the mkv version, you CAN use the audio from the mkv if you're going to convert it anyway. This is how I usually do it in Windows 7. You'll need to have 4 things installed:
Mkvtoolnix (we're using mkvextract to extract the tracks)
PX3's AC3 to WAV (a program used to decompress the ac3-file)
neroAacEnc.exe (Used to encode the wav file into an m4a-file. Not really needs an install, you just need to have the file in the same folder as the mkv file)
Yamb (An MP4Box GUI used to mux together the video track with the new audio track)
1. Open up a command window and cd to the path where the mkv-file is.
2. Extract the tracks with this command: mkvextract tracks "name-of-episode.mkv" 1:video.h264 2:audio.ac3
3. Use
PX3's AC3 to WAV to decompress the ac3-file to a wav-file. Name the wav-file "audio.wav".
4. Go to the command window again and write: neroAacEnc -ignorelength -br 192000 -if audio.wav -of audio.m4a
5. Start up Yamb and choose "Click to create an MP4 file...", then add the two files video.h264 and audio.m4a, choose a name for the resulting mp4-file and press "Next". When it's done, you're good to go! Works like a charm!