EDIT: I stopped remapping the keys with xmodmap and reset the shortcuts in Keyboard Shortcuts then my Play/Pause, Skip Forward, and Skip Backward buttons worked. Now if I can just get the Media button to work. xev says that pressing it is the same as button 2 which Compiz maps. I turned off the mapping and Compiz but it did not work. I am wondering if Nautilus starts the default media player when seeing the XF86AudioMedia key. I tried running a command as root and my UID but DBus does not start so I can't use my other buttons. Closer, but stumped.