I downloaded 3.1 yesterday, and all of a sudden all my music was gone! I looked in iTunes, and it all showed, but the Music app didn't show anything. This reminded me of an issue from back with 2.0. In 3.1 if you open Music after syncing it will "update Library" and will recheck the library. If your music disappears, just delete ONE song and put it back. This will cause the iPod to look for music again, finding everything!
