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Hmm, I do unmount (properly) before shutting anything down. But I still get missing files.

Hey, the same thing happens to me with my 750 GB Seagate FreeAgent. It's partitioned into two drives. 250 and 500 GB approx. They'll mount, but the files inside have vanished. I've been running Disk Warrior to rebuild the directories, and they reappear. I'm thinking it's a partitioning related...