I am sure this is a know issue and it appears to be without a fix. Each one of my MacPros with a FaceTime HD camera will not show up in FMLE 3.2 - Interestingly, the same issue applies with QuickTime Broadcast from Apple.
WireCast 5 on the other hand picks up the camera with no issues. It would seem that the only answer here is to wait for FMLE 3.3 or buy an external USB Camera. That does seem such a shame though.