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