Configure a difference in your X keyboard layout using the Keyboard Hardware and Layout system module's Advanced tab. E.g. enable Position of Compose key -> Menu. Confirm that this works by hitting Menu, then e, then ' to get an e acute é. Upgrade the keyboard-configuration package on your system. If you already have the latest, re-install it. Re-test the Menu key. It will no longer work until you unset and reset that binding in the system module dialog (or possibly if you log out and log back in). It seems upgrading keyboard-configuration applies the system-wide configuration in /etc/default/keyboard over any local settings you have. Obviously that shouldn't do so.