Comment 28 for bug 12153

I had a similar problem; I could assign Super as shortcut, but not use it as a modifier for a shortcut.

 dkr@eos:~% xmodmap -pm |grep Super
mod4 Super_L (0x7f), Hyper_L (0x80)

 I "set "Super is mapped to the Win-keys" in my
System -> Preferences -> Keyboard -> Layout Options -> Alt/Win key behaviour." as per above advice.

 dkr@eos:~% xmodmap -pm |grep Super
mod4 Super_L (0x73), Super_R (0x74), Super_L (0x7f), Hyper_L (0x80)

Now I can use windows key as a modifier key in keyboard-shortcuts(shows up as <Mod4>)