I've been following your trouble with this and I think you need to give us detailed information so that we can help you. I just clicked the little gear thing in the Vault sidebar of Aperture3, named it and picked a destination. Clicked OK and the update started. Something is screwy on your end.
What computer and OS version are you using?
mid2010 MBP upgraded to lion
What version of Aperture are you using?
version 3.2.1
What brand name external drive are you trying to use?
i'm using a 1tb 3.5" sata samsung drive taken out of my old desktop computer that i put in a case using high speed usb 2.0.
What connection does it use? (firewire, usb, wired or wireless)high speed 2.0 USB
What else are you storing on this drive?
Music, movies i have digitized, last 4 years of tax infomation, some important documents
What format is the drive? (Right click it and select Get Info. What does it say after Format)MS-DOS (FAT32)
I've had Aperture wink out on me using a Western Digital MyBook. It kept dropping the path to the Vault, but never had a format error. I use a Seagate Go Flex now with no issues. I think the drive in the WD is going bad. It kept failing Time Machine, too.
Dale