Lamest Keyboard Setting Ever
I’ve had to do this over and over again and I keep spending days looking for the setting. On many systems I’ve used, an xorg config that sets up the keyboard in a certain way (i.e. automatically) breaks and fails to map the windows key correct. This particularly has happened to me on Fedora in Gnome.
The fix for this is buried in:
System > Preferences > Hardware > Keyboard
Layout tab > Layout Options button
Alt/Win key behavior
I change this to Super is mapped to the Win Keys. Gnome’s frustrating sometimes in its lack of reconfigurability when compaired to many other systems but then when it presents you with options, they aren’t always obvious. I guess I don’t mess with gconf, where gnome’s registry-like madness allows much greater granularity, but really - who does?