Hi Jeremy,
This was a few years ago, and unfortunately I don’t remember what I ended up doing. Since this was just a fraction of my media that wouldn’t go back to Avid, it’s possible that I ended up doing an unpleasant workaround, like manually syncing the problem media. (Since I don’t recall a solution, this is possible.) If you are dealing with a lot of footage, this may not be particularly helpful to you. I’ll look into my e-mail history and see if maybe if I got some helpful information on an Avid forum.
Is your problem media from the same source/camera as the media that exported successfully? I believe the transcodes that I had problems with were converted from 23.98 to 29.97.
Evan