This totally mystifies me
 

I have successfully used SuperDuper in the past, but something has gone bonkers since I got my new Western Digital My Book Studio Edition (Mac).

Old setup: 1 usb external hard drive used for SuperDuper to clone to. Restores are successful and are bootable from restarts.

New setup: Still using the hard drive from old setup, but now is used for general storage. New hard drive uses firewire 800 and has two partitions: one for time capsule and the other (you've guessed it) for SuperDuper.

Problem: Given the new setup, when I restart my Macbook Pro, grey screen w/ APple logo appears, that's it. It hangs there. Reboot again, this time w/ firewire unplugged, os x boots fine.

I've checked with Western Digital's site and the hard drive is said to support fw bootability.

Have you tried FW400 or any other connection with this drive? (I generally don't recommend these troublesome MyBook drives...)