"I've had the problem if there are a lot of edits (like in Ep I and II) ... it becomes a long, tedious, mathmatical fix. You can speed it up in vegas by noting how many frames off the resulting audio is, then squeezing/stretching that many frames in Vegas and re-aligning your edits to match. It's not exact, but I haven't noticed anything being off when I do it."

Rikter and I had similar problems, and it turned out that the problem was caused by having loaded one of those codec packs (30-codecs-all-at-once kinda thingie.) I had done his Cure concert LD, and had to go through every few minutes and realign the audio to the video - and I had hardly done any edits to the original video.

I was planning on reinstalling Windows 2000 anyways, and doing so fixed the trick, but the lesson remains - don't load any codecs you don't need.