Audio exporting in different format than what's set on timeline

I imported some long xdcam video files with two separate channels of audio. For some reason some of the files imported as stereo (which I wanted) and some imported as mono even though I never made any changes to my camera. When I put the clips on my timeline I switched all of them to 'stereo' format, but when I export the file as an H.264 quicktime movie, the audio reverts back to the way it was originally on the clips. The clips that imported as mono play as mono, and the ones that imported as stereo, play as stereo.
I've tried things like switching the project default audio to stereo and even surround sound, but nothing seems to be working and I'm really at a loss. All I want is for my whole quicktime video is to have stereo sound where channel 1 article comes out the left speaker and channel 2 audio comes out the right speaker.

Did that, there's audio on both channels. Channel one is audio from a headset microphone and channel two is audio from the shotgun mic on the camera. I should be more clear, when I play it back in the timeline, everything sounds the way I want it. The channel 1 audio is only coming out of the left speaker, the channel 2 audio is only coming out of the right speaker, which is what I want. When I export, some of the clips revert to dual mono and I can hear a mix of channel 1 and channel 2 coming out of both speakers.

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- And http://blogs.adobe.com/VideoRoad/2009/12/using_a_flip_minohd_camera_wit.html
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Audio exporting in different format than what's set on timeline

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