I'm not experienced with the Intel data migration software, but since you're using Windows 7, do you have a spare portable HDD (with USB or other connectivity) handy?
To migrate my Toshiba laptop, I simply used the Windows 7 system image feature (located within windows 7 backup) and created a system image to a portable HDD. I then swapped over the laptop to my X-25 SSD, used the bootable recovery CD that the windows 7 system image backup process creates, and resotred the image from the portable HDD. It was quite a simple process, surprisingly, and given it was native to windows, I was pretty impressed. For the record, the recovered image on the SSD is perfectly aligned etc.
I know this doesn't help your situation directly, but it might be an alternative. Your issues sounds like the way the USB-to-SATA bridge presents the drive name/ID data to windows. I'd say its malformed in some way and hence the Intel software doesn't see the SSD it expects.