Long encoding times for footage captured with BMD H.264 Pro Recorder

Hi there,
I'm experiencing very long render times when encoding footage captured with the BMD H.264 Pro Recorder. Watching it encode (either through Premiere CS6, or AME) it looks like the encoding stops for periods of time. With other footage I can encode a 50 minute project in about 15-20 minutes, encoding with footage from the Pro Recorder is almost 1:1 in terms of project length/encode time.
The Pro Recorder uses QuickTime for H.264 captures, so don't know if that is causing issues. Don't seem to have the same issue with other H.264 formats.
System Info:
Windows 8 Enterprise (RTM)
HP Z820 with dual hexcore processors, 32GB RAM
Quadro 2000 plus Tesla for Maximus configuration
All latest updates have been installed (yesterday)
MPE is enabled for project
Also tested on a Z800 with Windows 7 and got same results
Editing the footage is fast and playback through timeline looks great. Anyone have a suggestion?
Thanks,
Jeff

QuickTime is still a 32 bit process and the 64 bit PP has to use a sort of "band-aid" to make QuickTime files work right. It's possible that might slow things down.

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