I ran Blender while hooked in to the registry and didn’t see any keys it accessed, so I think it only uses the file system for persistence of configuration. My recommendation would be to go to your blender directory and copy any thing you want to keep out of it (i.e. .blend files, etc).
Make sure you either have a backup of the blender directory of you have copied EVERYTHING you want to keep out of that directory. Then run the uninstall for Blender in the Add | Remove programs. Then go back to your blender directory and delete everything in there (this is why you moved your important files out of here).
Try reinstalling again… In a lot of cases files get left behind and mostly a hosed file got left behind. If this doesn’t fix it, the other thing I would try doing is going to your %UserProfile% directory. You should have some files here along the lines of:
I would remove those files and try reinstalling agian… .B.blend holds your preferences for when you start a new scene, so if you have anything special copy it out (but its possible it might be the problem).
Hope this helps… good luck man