I’ve just got why you should use new iTunes (8.2) since beta 5. They have replaced old iTunesDB library with new one based on SQLite, so sync is a bit odd thing now.
Device itself doesn’t use iTunesDB at all, but iTunes still does – I think it’s for compatibility reasons. When syncing, iTunes writes both iTunesDB and new library files to device. If there’s no iTunesDB file on device, iTunes will also purge new library and all your music will appear as “other” data.
I wonder whether new library will completely supersede iTunesDB or will they continue coexisting for compatibility reasons. But anyway, linux guys would be happy since SQLite format is open and much more clear for understanding.