I am seeing the exact same thing. My workflow is similar. I export QT reference file from the MC. I import to compressor and render out Quicktime movies in H.264 so I can pass through timecode(which is critical for my uses). So when I put the TC burn in filter in Compressor it renders black. Ugh
I would use Sorenson Squeeze but it cannot pass through timecode which is ridiculous.
Another alternative is to use CatDv -$99. Which can carry timecode and do burn ins while transcoding from QT ref.
Dan Lebental ACE