Well to override the what the PND is set to you can create an .ovr file.. this config file can be used to overwrite what the PND settings are.. This is kind of a pain to do this by hand. but there is a easier way using the Minimenu interface. Just select the Mupen icon and hit space.. there is an option "Set CPU speed for launch". This will create the .ovr file for you and start it at what you want it to be set to even in XFCE4 interface.