[Chris Schroeder]

I realize this thread is dated, but I discovered a workaround for this problem.

In AE, export your composition as a JPEG sequence. Open up the JPEG sequence in Adobe Premiere (when finding the files make sure to check “number stills” when you click on the first JPEG of the sequence).

And voila! You should be able to render the sequence in Premiere and then export it as a movie file.

I believe the core of this issue has to do with Quicktime codecs and this method will help you avoid any of that.

I hope this helps someone!