I know this post has been dead for a while but I found a bit of a work around. Not sure why it works but it does.
The flashing frames continued on a few other shots after a render out of CS4. I realised that all of the shots that had this problem originally came from Nuke (as Apple Pro Res). If I opened up the original Pro Res from Nuke in QT and exported again as the same size, same codec, then imported that back into AE and rendered the flashing would stop.
I’ve never seen this happen before and it seems pretty specific to this workflow but if anyone else gets this problem I hope this helps someone in the herd.
Cheers,
D