Audio levels go wacky when I export to AIF file?

I am working on a 13 minute multitrack project in Soundtrack Pro. I went through and set all the levels, then I export it to an AIF file and put it back into my Final Cut Pro project. Once I export, there are three scenes in which the audio levels go completely wacky - some places are at a lower level than what I set and other places are at a higher level than I set. I then go back into STP and when I listen back at those scenes these new wacky levels show up in STP. I then close STP and reopen and lo and behold the levels I orginally set (that I was very happy with) are back in place like nothing ever happned.
Some notes on what it might have to do with: All three of these scenes were shot using 2 Lav mics. These were each set into it's own channel on the Handy recorder. In STP, each lav channel is in it's own track. The audio level settings that I like for these two channels are very different (one actor was much quieter than the other). It almost seems as if in the export STP wants to put Channel 2 at the same level I have Channel 1 - which I don't want.
I have been spinning my wheels for hours trying to fix this. Anybody out there have any ideas or solutions or workarounds?
Much obliged for any help!
Michelle

This problem has also been plaguing me today. Here are my specifics and how I solved it (Expanding on what Quentin Holmes mentioned)
CONFIRMED WORK AROUND! The .m4v file gets created while encoding, but Adobe Media Encoder does not re-pack it back into the .mp4 unless you select the "Export Audio" in Adobe Premier export prior to queuing. If you don't want audio, mute the individual tracks and still export audio.
My details:
Just bought a GH4, shooting 4k 25fps MOV, trying to simply trim a few clips and export them as H.264 .mp4 with no audio. (By the way it would be nice if we could export 4k .MOV files from the camera back into .MOV once finished editing, but in premier that frame resolution is not supported)
Specs: Mac Mini, Quad Core i7, 16GB Ram, OSX 10.9.4, Adobe Premier Pro CS6 6.0.5, Adobe Media Encoder 6.0.2.81
Hope that helps anyone with the same prob

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