I fiddled around with emplode for windows (instead of my regular emptool for linux), and after syncing I found that my unit now works correctly! That is to say, it does not rebuild the music database anymore.

Right. That's because it needs read-write access to the disk in order to fix things. When you boot it up normally (such as in the car), the disks are read-only, so the "rebuilding music database" thing is only temporary.

When you perform a synch, the disks are mounted read-write. So when it rebuilds the database as part of a synch, it's got a chance to fix whatever problems it's having.

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Tony Fabris