Here's some more details:
I'm viewing the export in the preview panel in After Effects or I will encode a portion of the project as a sample and then view it after...both with the same result.
I'm running CS5 with Windows 7, My source footage is .mov from a Canon Rebel T2i shot at 1280x720 with a frame rate of 59.94. I also have a couple of .png images in the project. The problem happens only during export and rendering, not during normal playback in the editing workspace.