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Well, if it's always the same file, then most likely one of the source footages is really damaged. The error not occuring every time mustn't mean anything. If the element in question is not visible at the given frame or AE doesn't do anything with it because it isn't required, naturally the error would not occur. I'm afraid the only way to track this down is to selectively disable/ remove the sources from the comps in question and render some test clips. Perhaps it would also help to check all the files used in the project in a "neutral" app such as external image and video viewers (XnView, VLC, MediaPlayer Classic...)
It's not always the same source footage. For each project we render out new proxies for the compositions, and the error occurs with certain comps, but not always -- and they're always visible. If we don't render proxies then then the project is fine, but we need them for our workflow.
Well, what CoDec/ format do your proxies use? This might be simple breakdowns in the data stream of QT files or something. Have you tried different methods?