Are both those files located in the same spot on your computer/network?
I considered that as well and sadly yes they are so that doesn't solve things.
I think I have found a clue and it involves the fact that the original filenames of these files was actually much longer and included symbols such as brackets "[ ]" and dashes "-" and I simply renamed the files in finder in case that caused AE to have trouble reading them.
Now it's occurring to me that files with those long names were actually corrupted upon rendering. Corrupted just barely enough to make AE struggle to work with them but not enough to mess with playback in finder or QT.
Another clue is that these files also struggle when being transcoded in media encoder. The encoder transcodes easily until apx. 99% at which point I stop the encoding and interestingly the transcoded files work better than the originals.
So perhaps there was an issue with the very end of the file's and when that is ignored in transcode they work better.
Are you still facing this problem? If not, let us know how you solved it. If so, please let us know so we can assist you further.