The only suggestion that I have is to play with ~/Library/Preferences/com.apple.systempreferences.plist. Rather than trash it, move it to the desktop (or other location) and then log out/in. This should reset all System Preferences to defaults. If the problem is solved, you'll have to reset every system preference. If it is not solved, put that plist back and log out/in again. That will restore the other preferences.
If you have Applecare, you might want to call Apple. Even if you don't, you might want to call although you'll have to pay.
In the meantime, someone else might come up with a better idea. Good luck and let us know how it goes.
FWIW, there is no System Configuration folder in ~/Library/Preferences in my setup.
EDIT: ~/Library/Preferences/ByHost has a bunch of plists that start with com.apple.systempreferences... You could play with those as well. I have never done this but if you take care not to trash anything, you can always put them back.