We have been getting this message on one of our Avids. We are using HDCAM HDW-S2000 Sony decks AND the tape I am capturing is a complete master of a show (done in a linear suite) that was blacked and time coded before the edit. We have house sync and it seems to be only one of the Avids that has this problem.
We are using Media Composer 5.0.3, we have not upgraded since we would also have to upgrade Interplay and THAT is too expensive right now. We use house reference.