Render glitch?

Hi,
I'm working with characters shot with a Canon DSLR (1080P), edited in Pr, sent to Ae (via replace with Ae comp), but they are not intended to go back to Pr because they will be rendered out as a png sequence in Ae, then printed for a stop-motion piece via contact sheet in Ps.
Phew!
My goal at this point is to roto/mask/luma key the footage then render it out it for print. BUT, it does not render it out correctly. It actually erases some of the image (check out his jeans), one of my parameters isn't being reflected in the render. See my attached screen shots of both my monitors with a rendered QT file open with the playhead in the same place as the composition. I tried rendering out a png sequence, animation codec, and h264 codec. All produced this result frequently in different areas of the composition.
What could this be?
I'm printing these characters out card stock and then cutting them out indivdually. If anyone knows of a better way of preparing the files please let me know.
FYI: The original footage is 23.98fps, but I change the composition settings to 12 fps.

Here is a screen shot with full reselution ram preview

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