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Check your media cache settings. You are probably simply running out because the files are conformed over and over with every operation, even if they are based on teh same source. Probably some ugly bug that has been sleeping there without anybody ever noticing. If that's the case, then I'm afraid short of continually purging the media cache to avoid these overflows there is nothiung you can do. Converting teh files to a format that doesn't use the MC like Quicktime files might avoid it entirely, though.
Hmm, might be, the files i'm using are H.264 MP4's. I would prefer to keep them this way, as I've grown rather fond of the format for the quality/disk-space/performance-in-adobe balance.
So quicktime MOV's don't use MC? No matter what codec is actually inside the container?
The CoDec still matters. A H.264 QT is treated just like a plain H.264 file. If you have the time and resources, still try this out by converting some material to QT Animation or PNG. That's the only way to be sure. One thing that also comes to my mind now that I think about it could be invalid timecode in your files. Since CS5.5 supports source timecode, it may frown on discontinuous TC. Try to work wuth those options turned off then...