Here's a couple of possible fixes:
Go to Displays (not visible, so SwitchResX should work), change your screen resolution to anything different, then change it back. That should bring back off-the-screen windows.
If that doesn't work, try the System Preferences menu, then change the sort (under the View menu in System Preferences (Organize by) to Categories or Alphabetical, etc. Change it back when the window is fully in view, if you like.
If neither of those work, then I would suggest going into your user folder, Library, then the Preferences folder. Delete the file com.apple.systempreferences.plist
Log out of your user, then log back in. Launch System Preferences. That should do it!