Have you demultiplexed with DVD Decrypter? The results will probably be the same, but it's worth checking out.
If it's still problematic, I've often figured out the number of frames that a film is "off" and then, every X number of minutes, cut or repeated a frame right on a shot change to fix it.
I think it has to do with Womble editing 23.97 fps at 29.97, doing it's own telecine on the fly. But that is only a guess.
I haven't had the problem since I've been generating stereo reference files, then re-creating the surround mix in Vegas, but the source material has remained in sync for me. The sync problems were always with exported content in my system.