Bob, Ian,
I’ve been having the same problem with CS5.5. I see the problem with clips coming from AE as you describe. I’ve had the problem exporting from PP through AME with a variety of different codecs (Animation, ProRes, Motion JPEG, Cineform, etc. I don’t seem to get the problem with H.264.
There are two things to try for a workaround. First, render the work area. I’m not sure why, but this was the advice from Dennis Radke in the Adobe PP forums. I can’t say it resolved my problems. The second thing to try is to Export directly from AME rather than Queue the clips. That seems to be the most effective.
If you find another foolproof way to eliminate the problem, I’d love to hear it. It’s been a major hassle for me lately.
Thanks,
Jay