Adobe Audition audio won't sync

Hi there,
We've been editing with FCPX for a while now and it's gone smoothly for the most part. Typically we've been recording video with a T3i and our audio via Logic or a Zoom portable recorder. I've never had a problem dropping the alternate audio over the camera audio and syncing it up... until now.
I used Adobe Audition on my PC, because I was in my office and not the studio. When it came time to comp the video and audio together, the audio file (.wav or .aiff I tried both) would lose sync by the end of the 9 min clip. The strange thing is that the waveforms for the in-camera audio and .wav file lined up perfectly in FCPX, at least visually.
I eventually found out about the 99.9% trick, which I couldn't do directly in FCPX, but could emulate by moving the Retime handle slightly. When I was done, the track seemed to sync perfectly, but on export had an out of phase type sound to it... sort of like I added a room reverb or something. So, that wasn't a useable solution. Strange side note, the phasing sound would never be there on initial playback, but start after about a second or so. Weird!
I ended up manually tugging the audio, the sync issue was that the audio ran about a second long, every time I cut to my B roll, keeping things lined up. It wasn't pretty, but it got the result I wanted.
Now after that wall of background text... what the heck is going on? Why would Audition output a file that somehow loses sync over time, even though the waveforms seem to line up perfectly?
Is it a setting in either or both programs?
Thanks in advance for any insight you have!

Audio interface
iMic USB Audio System
MIDI interface
EDIROL UM-1EX (by Roland)
Keyboard controller or synthesizer
Alesis QS 8.2
How is all this linked
Alesis > EDIROL > Entrega MacHub4U USB hub > USB port on back of G5
Where is audio input
Shure SM58 > iMic > USB port on front of G5
Where is audio output
Alesis > Creative speakers
iMic > G5 > Klipsch speakers via port on back of G5
Sorry I didn't think to give this info in the first place.
Thanks for your help.

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