Did you daisy-chain the camera to the drive? Very bad practice.
I saw this problem years ago at my film school. With an older Sony DV deck (DSR-20, I think) using FireWire, when a FireWire drive is hooked up to the computer at the same time as the deck, on the same set of buses, whenever the deck's auto-off kicks in, it sends some kind of signal to the drive that fries the directory of the drive and corrupts concurrently open project files. DiskWarrior was what we had to use to rescue the drives.
If you're forced to hook up a camera and a drive without a separate FireWire card on your computer, don't ever turn off the camera with the drive mounted -- dismount it, turn it off and disconnect the drive first.