In the process of hunting the problem down I noticed that the second film is about 1 frame out of sync.
I THINK I fixed it, but I'm not trusting anything right now. Unfortunately I now have to sit through the film again.
Not that the movie sucks, it's just I'm really tired of it.
It LOOKS like the problem is M2 has a slight audio delay. Which means both M2 and M3 needed to be tweaked.
Looks like another marathon for me. Sigh, this project won't die.
It looks like this might end up being an anniversary release after all, sorry guys.