Your described behavior resembles something that happened to me when I was trying out one of the V3 Alpha builds. Are you running 2.0 final or V3 alpha?

Probably a moot point, though, because you've got hard disk trouble. In terms of the unit keeping its playlist data, very little can be counted on once you've started having disk trouble. Sure you could reload everything, but if you're having disk trouble the problems would just come back.

As Mark said, a boot log would be very helpful.