My best guess would be when booting off the USB hard drive your computer is looking for the first partition it can find and trying to boot from that. In this case that partition would either be your empty one or your media and obivously there isn't an OS there to boot. Now how you would go about fixing that I couldn't tell you (aside from wiping the drive rearranging the partitions so the Backtrack is first). A 8GB USB drive can be found for around twenty bucks and make for a great way to run Backtrack. Either that or you could run it in a VM environment. Good luck!