I'm running Ubuntu 11.10 using the gnome-fallback mode with compiz.
My keyboard is the Apple metal add-on USB keyboard. My .Xmodmap file is set to swap the Alt and Command keys.
I built the key map into a .Xmodmap file, and it works successfully for the X session. (I can do Grid commands with ctrl-alt-number pad commands using the Command key as the Alt key.)
But none of the applications running under X recognize the new key mapping. (Command-F doesn't open the File menu but option-F does. Command-right-click doesn't open the panel menu, but option-right-click does.)
How do I get my apps to pick up the new mod mapping?