Usually deleting studio.xnf will fix the problem, so always try that first. I recommend making a backup copy with your settings after you get things working.
I've had to do more than a couple reinstalls, I've had scripts crash that cause like 10 playlists to show up in the playlist editor, all with zero items. And the db has wigged out before, as well. But 2.5 has been pretty good in terms of reinstalls, I don't recall having to do it.
Install it to a clean directory, then move your skins and scripts over, then delete the old directory. If that doesn't fix it, there's more going on than just Winamp issues.
I was away for a while.
But I'm feeling much better now.