Ok, icky fix, but it works. It was in the first place I looked, it just seemed like it was a bad idea. There are 26 named commands that get treated special and have their default hotkeys listed in menus, such as "File>New Ctrl-N" in Maya 2012. These are the hotkeys that will revert back to default behavior if you have…
I'd like to just kill off the part that appends the hotkey inside the menus, but can't find that part so far. Assuming that it's in the scripts and not code. It only does this for default keys marked as NamedCommands. Cool it worked for you square.