It's a result of the compression in the codec - that's why you don't see it when using Animation, as it's essentially an uncompressed codec - which is also why it's so large. I would try ProRes 422, which is much lighter than Animation but still essentially uncompressed. It really depends on your final delivery target what codec you should use.
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Mark Spencer
Freelance Producer/Editor/Motion Graphics Artist
Apple-certified Master Trainer
Author, Motion 4 from Peachpit Press
http://www.applemotion.net