Found this on the Apple forums:
"I found the problem with my movies was that they didn't have the right profile. If you look at the specs for h.264 movies for the iPad:
"H.264 video up to 720p, 30 frames per second, Main Profile level 3.1 with AAC-LC audio up to 160 Kbps, 48kHz, stereo audio in .m4v, .mp4, and .mov file formats"
A lot of my movies, even ones that were Apple TV compatible, were of profile level 4.1 or 5.1. You can see what your movies are by downloading the free program MediaInfo which which tell you what profile your movies are. All of the synching issues I had with movies came down to them not being 3.1. I'd imagine if you ran your movies that won't sync through that program, you'll find that they aren't perfectly in line with that allowed specification."
So, the question I guess is how to drop the profile...