has anyone found a work-around for the mkv audio sync problems?

There's a well known issue with plex/XBMC/boxee programs where the audio slowly gets out of sync while watching MKV files. It seems to be a random thing and doesn't always happen with every DVD converted. I understand that the next version of Plex will address the problem. The only way I've been getting around it is to use MakeMKV and then take that file and run it through tsMuxerGUI and then point plex to that folder. And then when they finally fix the issue, I'll just get rid of the tsMuxer files and use the MKV ones.

Is there any other way for a work around? (Yeah, I know that there's Handbrake, but the thing I really love about MKV is that it preserves the chapter stops.)

Well, the problem (and has it has been discussed in plex and XBMC forums) seems to be a random thing. Some movies play back perfectly and others start to lose sync about 45 minutes to an hour in. I've emailed Elan, the guy who made plex and he is aware of the problem and said that it seems to run throughout all of these programs and hopefully will have a fix for it in the next version. I do hope so. It would be a lot easier to not have to burn and convert the same movie twice!