Well let's see, there are about a zillion different ways you can encode video and there are some known bugs with QuickTime .png compression in the latest build on some systems so without details I can only guess that you have run into the Quicktime bug. You can try transcoding (changing) your video to another format using the Adobe Meida Encoder and see if that helps. I would pick a good, stable production format over a highly compressed format like h.264.
If that does not fix the problem then we need to know exactly what kind of compression was used in your video.
Thanks for the response! I think I'll try to just replace them with a .tiff sequence... Which I'm now realizing I would have done with AE. Perhaps I can try that approach via Premiere... or take it to work and see if I run into the same issues.