I am having this exact problem. I regularly log and transfer P2 material into my final cut projects and have never had a problem. This time when I used log ad transfer the quicktime files in my scratch as well as the clips in my timeline are out of sync. I am using an older hard drive to pull the video from and I am suspecting that the transfer rate of the hard drive is too slow or something. Let me know if you have figured out how to correct this problem.
Thanks