Issue with Quicktime Reference Files

I am experiencing an interesting problem with the Quicktime Reference Movies generated out of Tentacle Sync. Let me explain: When I use Tentacle Sync to generate QT Ref movies of my synchronized material the resultant files play back perfectly in QuickTime 7 Pro until the point where the RAID has to be ejected or the computer restarted. After disk ejection or computer restart, the QuickTime Reference movies have missing audio and video tracks from the original camera clip with only the TC track and the audio from the external synchronized recorder as  below.