Ok, here's how to do it, for future reference. I think in my case the problem was the frame rate. It was set at 24, but as per http://support.apple.com/kb/ht4025, apple likes 30fps for a 640px movie.
So, if this happens to you, run it through MPEG streamclip (it's a free download) and convert it to 30 FPS Jpeg mov files.
man, such a relief! I hope this helps others.