Thank you for your bug.
Compiz overrides the key settings in System>Preferences>Keyboard
Shortcuts however these keys still work if compiz has not used them for
anything else.
Specifically for alt-F2 you will have to install compizconfig-settings-
manager and modify the keys compiz has configured for the run dialog:
System>Preferences>CompizConfig Settings Manager>Gnome Compatibility
** Changed in: compiz (Ubuntu)
Importance: Undecided => Low
** Changed in: compiz (Ubuntu)
Status: New => Triaged
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Compiz overrides custom keyboard shortcuts
https://bugs.launchpad.net/bugs/257878
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