Crossfades don't export smoothly

Hi everyone,
I've got a large multi-track edit of a pipe organ recording. We've edited the piece with cross-fading different takes to make one succinct song. I've found though that once I'm satisfied with my cross-fades, they don't always playback smoothly in a consistent manner. I've found also that they don't export well. When I play a two-track mix of the piece for CD, the edits either don't play smoothly or they have little clicks and pops in them.
Is it a latency issue? Any suggestions as to how to get these to export play smoothly?
Your immediate assistance is greatly appreciated as we need to get a master out quickly for an event.
Message was edited by: HomeVideoStudio

No, they're each a second long or so. The timeline is merely zoomed out all the way out to show all the edits, which are crossfades into another take.
The creation of the crossfades are not the problem. Playing back the file is typically fine, the problem is exporting the mix. When the multitrack is mixed down to stereo, these transitions are very audible (clicks, pops, etc.) instead of the seamless transitions they should be.
Anyone know why this wouldn't export smoothly over these crossfades? It's never been a problem in Digital Performer or ProTools.
Your urgent response is appreciated. We've got to wrap-up this project.

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