Here is the video:
http://www.youtube.com/watch?v=cjDEFlQ6A0o
The video is of a constant zoom into a Fibonacci spiral. The glitch is that the top part of the centre area will occasionally move up. I have no idea why this happens, as it only does so in the exported video. In After Effects those parts look fine.
I made this scene by making four 28,000 x 17,500 px precomps of Fibonacci spirals made of flowers. They were made that large so that the smallest quarter circle of the spiral would be able to fill a 1080p frame without interpolation. To achieve the zoom I attach the precomps to a null object, and arrange them so that there are no seams between the different individual spirals.
I'm using CS 5.5, but will switch to 6 soon. If that doesn't help, I could theoretically export the precomps as AVIs and then work with those. Does anyone have any ideas as to why this glitch is coming up?