Media Encoder CS6 Not Exporting all Audio Tracks From Premiere

I'm working with DSLR footage, 2 Channels of .WAV audio from an exernal recorder (H4N), and a 1 channel .WAV Music track. 3 Channels total of .Wav audio.
I can export from Premiere Pro CS6 to H.264 just fine, but if I try to send it to Media Encoder, it only track 3, which has the music.
I can't figure out this issue, and haven't found an answer on any forums. This problem effectively makes Media Encoder useless to me, so I would prefer it to be solved, rather than find a work around.
Thanks in advance for your help!
Mark

I'm having the same problem. But even worst.
For the test, I take a 10 min .mov or mp4 file, simply modify the "scale", and hit the export.
a 10 min file is taking 4 hours to render.
This is on a:
2012 MacBookPro i7 2.3Ghz, 16 GB 1600 DDR3, SSD disk. - Mac OSX 10.7.5
and a:
2011 iMac i7 3.7Ghz, 16 GB 1333 Mhz, 7200 RPM HD - Mac OSX 10.7.5
The CPU stays at 90% idle the whole time.
I know this is an old thread, but maybe someone could give me a hand.

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