I can assign Alt+F1 and Alt+F2 to any function I like in the keyboard configuration window, but its not beeing used. Alt+F1 is always 'dash home' and Alt+F2 is always 'run'
I sat with the same issue after upgrading to 12.04 and installing Gnome Shell. I tried to disable Alt+F1 from wherever I could, to no avail.
As I was about to give up I found this gist: https://gist.github.com/2402448
Credits to https://gist.github.com/musinsky