Sound effect is out of sync

Hey all,
I'm trialing Premiere CS6.
I have my sequence, about 1:20 with many video clips and tons of sound clips. I exported the sequnce to a pro res 1920x1080 24p, uncompressed audio.
The entire thing is pretty much perfect, as far as I can tell, except for ONE sound clip which I know is not in the right spot. It is a slow tension crescendo that has been speed up (with pitch mainatained) to fit within my video clips. When viewing the exported file, the audio clip reaches it's tension climax about 1 second or so before it should. In the timeline, it lines up perfectly.
As far as I can tell, this is the only sound clip that is out of sync, which is really weird.
Anyone know what could be happening?
Thanks
Specs:
MBP C2D 5.53 8 gb ram

My bad, I was always under the impression that H264 was a type of quicktime format and thought you meant to export to a different uncompressed format.
I'll give it a shot, tried to adjust a few things to see if that makes any difference

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