I have a new Seagate USB 3 2TB external drive. Partitioned it and installed Ubuntu 13.04. When it is plugged into the USB 3 connection the drive is found by the file manager of my 'host' Ubuntu 12.04 system and works ok as storage but is not found by the computer when booting so I can't boot from it. It does not appear in the list of available boot devices in BIOS. However, if I plug it into a USB 2 connection it is found. It appears in the list of available devices in BIOS, it can be booted from and works normally, but maybe just as a USB 2 drive. The problem seems to be pointing at some BIOS setting, maybe.
I have an ASUS M4A87TD-EVO motherboard and X6 1055t processor.