I've had this problem with 3.0 and the URL structures it creates for the Multisite sub-sites, and after much messing around it seems a full reinstall is the only way to go.
For posts I know I can just export and import.
For theme customizations I could just save the theme folder on my drive.
But what about URLs? If I reinstall WP and put it back on the pretty permalinks I had before...will they still work when someone clicks a link from the net somewhere?
Other people have also been having this funky URL structure issue but there doesn't seem to be any good solutions. :\
Also, I already tried the reinstall button located in the updates section. It fixed the issue for a couple minutes, but the URLs went right back afterward.