hi dave, I recently had the same problem again, and solved it in the same way:
I had to backup my internal drive (say disk1) on a friend's external drive (disk3) different from the one I use for daily backup (disk2)...
so I backed up disk1 to disk3 using "erase than copy" and everything was okay..
when, some days later, I plugged again disk2 SD! said it couldn't find disk3...
I selected disk2 and launched the backup with "shutdown" option, and it FAILED to shutdown at the end of the backup...
as the first time, everything was solved with Onyx cache deletion.
I can't try now becouse I'm really busy, but I think the steps to reproduce the problem could be the followings:
plug a (firewire) drive > launch SD! and "backup, all files" on it with "erase than copy" > restart (dunno exactly, about week was passed in the meantime) > plug a different (firewire) drive with a different name > launch SD! (it will tell you that can't find the first drive) > select the second drive from the dropdown and perform a full backup with shutdown option...
if the Finder fails to shutdown the computer as I expect, try to delete caches (dunno what kind of cache does the job, in Onyx "automate" panel I selected both system & user caches)
really hope this helps finding out the problem
