My databases were all on drive 0 - nothing on drive 1.

Keep in mind that the playlists and the databases are two different things. The databases get built from the playlists, and it's possible you might have playlists scattered among both drives. A temporarily-missing drive1 (say, because of cable problems) might cause the symptoms you describe, especially if it was MIA during the database rebuild.

I'm moving to Alameda - you anywhere near there?

Nah, I'm on the other side of the state, near Lake Tahoe. But I go to all the Bay area meets.