Random Audio Levels Change Exporting STP to Aiff Master

I've been mixing a feature film scene by scene (STP can't seem to handle a full feature mix at once due to memory problems) and generally pleased. However, I've noticed on two out of 10 scenes mixed so far, when I exported the aiff file as a master mix, audio levels on various clips (not all) drop considerably in the mixed file. Even clips in the same track lose audio level in places in the mix, seemingly randomly. It's very weird. Then, when I listen again in STP the levels have been mysteriously dropped as well. NOT the volume slider bar. It stays the same. No change in gain. All LOOKS as it was before exporting but the drops are there. It's as if the exporting process has done something to the STP timeline levels without visually changing anything. If I change the layout screens or play around with the submix locations, all returns to normal in STP. But after I tried exporting again, the same problem happens.
I couldn't find any other forum help with this. Some people suggested 'Render to Action' or 'Flatten Audible Actions' for a similar problem someone else posted, but those options are ghosted out on my multi-track project.
I tried deleting all .plist files related to audio, soundtrack and final cut studio (not easy to find, may have missed something). And this problem doesn't exist on some other scenes using the same process which worked fine.... so it's extremely odd.
I am using minimum filtration, just a limiter with -4.5db and 3db of gain on one track. All dialogue going to a submix and all fx to another. There are only 4 tracks of audio in the mix in question.
I 'analysed' and 'fixed' all phase issues in clips. No change.
The original recordings are .wav files from a Zoom H4N set at 44.1 hz, but that's the same in all scenes, so not sure why only two would make a problem. (the project itself is set to 48hz)
I'm fairly experienced in FCP Studio but getting a bit loony over this one, so hope you can offer some help. Please don't suggest using other software like Pro Tools for this mix. It has been working fine and I'm happy with 8 scenes. There must be something simple going on with the 2 odd ones.
Thanks, Ken STP 3.0.1 Snow Leopard, Intel Quad MacPro
'It's not a question of becoming. It's a question of uncovering what you really are, of letting everything that is not yourself fall away'. - Journey to Ladakh
I think this applies to editing as well....
Ken Barnes, Producer, Director, Editor
www.blissmonkeyfilms.com

I may have found a clue, but still don't know how to fix it. The file from FCP to STP was a stereo file with mic A on left and mic B on right (used a Zoom H4N). I split the file in STP into two mono files and separated the tracks. So actor A is on track 1 and Actor B on 2. All levels fine. I checkerboarded the tracks so there wasn't a lot of overlap. So far so good. Somehow, STP seems to be reading only Track 1 when it does the export; the level drop I'm hearing seems to be Actor B appearing on Actor A's lavalier, even though that data has (supposedly?) been chopped for the checkerboarding. Is this clear? IOW, even though the timeline shows clearly distinct and clearly audible separate mono tracks 1 and 2, the export mix isn't reading it that way and ignores my separation of stereo to 2 mono tracks, preferring to read from only one of the stereo tracks (or possibly only Track 1, but not throughout the track, only where the checkerboarding has occured). And then it somehow 'remembers' the export when it re-opens the project until I make almost any adjustment in STP and it magically returns to normal. Help!!

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Random Audio Levels Change Exporting STP to Aiff Master

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