I've had this problem lately. It started after the latest FTM 2012 update (not 2012 overall, but an incremental update). Over the summer I was able to easily migrate from PC to Mac (which is my backup machine). Now, when I use the migration tool, the 69mb PC file converts to a 136k Mac file! Obviously, it's not converting anything but text.
I wrote up a support ticket but they basically told me there are no known bugs of this type. The older pre-update files I have still convert fine; the newer stuff is useless. I'm not sure which update made the problem- FTM or the Utility tool itself. I think I still have the older migration tool on CD, so I plan on trying that out.