[dan jones] "The files are on the hard drive and not on SxS cards. Could that be the problem?"
No. I always run Transfer on files I've already copied off of the SxS card onto a hard drive.
Unfortunately, I've never encountered this issue, so I'm out of suggestions. Other than suggesting you also post this over in the XDCAM forum as well.
http://forums.creativecow.net/sonycinealtahd