Alright so I have 12.04 installed on my macbook air and somehow it is not recognizing any key as being the Super key both the Option key and the Command key are coming up as an Alt key. I have no idea how to fix this.
I had the same problem as you and I solved it by changing the ~/.Xmodmap file to the one provided by dfacto. It is not perfect (the alt and super keys are switched by default, and it changes the trackpad to "natural" scrolling) but at least you have a super key. I guess that by understanding how Xmodmap works, this can be solved.