Just made an account. Harmy, you and everyone who has contributed to your projects are awesome by the way.

I had a similar problem, the audio was fine in the mkv but after being burned it was out of sync by about 1000ms...

Actually, I got the mkvs from torrents and ran into problems besides the audio sync. MuseR didn't want to accept the mkvs at all unless I passed the file through mkvmerge. And then, it played fine from the LG drive but would streak when played from my old HP player. I put the mkv through SUPER (without audio, I could get the tracks back in with mkvmerge). Not ideal for sure but paid close attention to the settings to get the best output i could from the source. Fixed the problems I had.

Star Wars just needed to go through mkvmerge once before tsMuxeR would like it.

Empire and Jedi had the streaking issue and I sent it through SUPER before tsMuxeR.