I’m gonna have to back off here (BetaSP to D1 to AVID DV to QuickTime MPEG-2 spells trouble to me), rest assured, you’re not the only one who’s pulling their hair out over this.
The one last thing I’d try is to not perform any cropping and export the clip from the Avid ‘as is’, see if Compressor can detect it correctly and do the right thing.
I’m sure there’s somebody on this forum who’s been through this – Ben?