My editing co-worker and I have been having this problem for sometime and neither one of us can figure out what is going on because it doesn't happen all the time.
When rendering from AE we have been having a problem with color changing on imported video. At one frame it looks great and then the very following frame it gets dark and stays that way for the rest of the render. It looks fine in the preview and it doesn't matter what kind of video file it is(SD/HD). The change always seems to start at the first few seconds of what is being rendered. We always use QT movies for imports too. So any insight would be extremely helpful.