Have you installed the After Effects CS5 (10.0.1) update? That update fixes a lot of problems, including some problems with audio.
Also, please give much more information, including operating system, video and audio types (MXF is just a container type, and the audio and video can be of just about any format), third-party codecs installed...
Thanks Todd the 10.0.1 update did the trick!!!! The audio is now in sync in both tracks.
For what it may be worth this is what I do know about the files provided from my client (they are not available over the weekend for more feedback). I tried pulling the data from Bridge and from the Meta Data window in AE but there was nothing of value reported in either.
The footage was shot with a "Sony Camera" (I wasn't given the model)
I was given 2 version of the footage one in Quicktime where they specified that they used the XDCAM EX codec [XD CAM EX 1080p24 (HG)]
I assume the MXF files uses the same codec.
Frame size: 1920h 1080v (1.0000)
Frame rate: 23.976 frames/second
Pixel Aspect Ratio: Square Pixels (1.0)
Fields: No Fields (Progressive Scan)
Audio Sample rate: 48 KHz (24 bit stereo)
As far as my system goes:
Vista Ultimate 64 Bit OS - Service Pack 2
Intel D975XBX2 Motherboard
Intel Core2 Quad Processor (Q6600 @ 2.40 GHz)
8 GB RAM
Thanks again for the help....Bob