I have been having the exact same issue with C300 footage. The audio on some clips is out of sync and cuts of early before the vision ends. Thus meaning you cannot simply slip the audio back into sync. I never had this issue on Premiere Pro CS5.5, so its somethign recently that has caused this issue to arise. If I play the offending clip in VLC player it play correctly with its audio in sync and running the full length of the vision.
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