I have to ask... why are you torturing yourselves with converting program streams to transport streams.
I was actually referring more to AVIs that I've converted, and a few TS files that had choppy audio.
As for using CinemaSix, I actually find it more annoying to lose audio sync when it switches to the next vob, than I do the process of converting the VOB to a TS. I've actually been successful with converting a VOB to a TS with VLC, then using HJSplit to split it into smaller chunks. When this works, it's much nicer than using TStoATSC, because you end up with 1.5 gigs of TS files afterwards rather than 7 gigs of TS files (on a 45 minute show).
I absolutely love the "Rotate button to recover sync" functionality of CinemaSix, but it always skips ahead 3 or 4 seconds in order to achieve the re-sync, which, by the time I've gotten hold of the remote and gotten the Rotate button to register, I've lost a good 20 to 30 seconds of audio on the stream. And I have yet to figure out (if there is a way) how to get CinemaSix to skip forward/backward to the next/previous TS file.
TStream, so far, has crashed on me more times than it's worked for me. Really looking forward to that one getting stabilized! Keep up the good work!