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Are you absolutely certain that the video was captured to the computer in "raw." Are you sure it wasn't compressed? If you capture a video to a compressed format, do your editing to that video and then render to yet another compressed format you will get all kinds of artifacts. My suggestion is to see if you get the same results with a different computer using Final Cut (or some other pro-sumer level software).
In the PC world you want to stay in AVI format (uncompressed to be exact) until the final render. I'm not sure if this is true for Macs. Just be absolutely sure that your video is in an uncompressed format while editing.
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