Premiere Pro/Media Encoder fail when exporting something with AE linked?

Hey all, I do some video production work for a university, and we're running into some problems when trying to export all the videos from a particularly large course.  We haven't run into this issue before so I'm hoping someone might have knowledge of it and can help me out.
Here's some background-
I'm trying to export videos, about 20 minutes each.  Each video has an opening sequence and closing sequence that were created in After Effects and are Dynamic linked in the right spots on the timeline.
We're encoding with Vimeo HD 720p 29.97 settings.
Media Encoder gets through one pass seemingly just fine, and then a little after halfway through encoding it stops (doesn't crash, just stops encoding any further) and crashes when attempting to stop the queue.
It's a pain to export from After Effects and re drag in all the sequences, so our workflow keeps all exporting Premiere -> Media Encoder.
EDIT: Can't believe I forgot to mention this- works fine exporting directly from a timeline in Premiere, it's only when Media Encoder is used that issues arise- but it's unfeasible to export 30 videos from the timeline.
EDIT: Done some more testing over the course of the day.  I can add After Effects files to a AME queue and encode them with the Vimeo settings and it makes it through both passes, correctly exporting the videos.  It just doesn't work when those same compositions are exported as linked compositions in a Premiere Pro timeline.
Some things I've tried with no success:
Exporting the After Effects files separately does not work, it hangs even if only exporting the after effects segments.(20 seconds each).
I've turned off CUDA and done software only, still hangs.
I've tried dragging/adding from Media Encoder/any number of different workflows to get the sequences from Premiere to After Effects.
I've tried exporting with different settings: (e.g. non Vimeo HD 720p 29.97), still hangs (doesn't even start encoding, doesn't get halfway).
Any ideas?

I experienced this at one point.  Searching the WEB I saw suggestions that there was a problem with a recent version of Quicktime.  (I have no idea why the quicktime player would have an impact.)  However, reverting to an earlier version of Quicktime fixed the problem.  Search this board using quicktime as a search phase.  The quicktime web site allows you to download the earlier versions.  I'm not at my editing machine, but I believe that I am at version 7.5.2.

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