I just upgraded from 12.04 to 12.10 and my desktop was fully reset to the defaults. Rather annoying.

The worst part is that I tried to do things such as reassigning the Alt-F1 and Alt-F2 keys and it did not work. Somehow the default Gnome keys remained in effect!

I found the solution on Ask Ubuntu.

gsettings set org.gnome.desktop.wm.keybindings panel-main-menu "[]" # disable Alt+F1
gsettings set org.gnome.desktop.wm.keybindings panel-run-dialog "[]" # disable Alt-F2

Editing the preferences did not work at all.

Source: https://askubuntu.com/questions/126817/how-to-disable-alt-f1-alt-f2-shortcuts/348607