Okay, had a look at the problem - it's essentially just a problem with the level at which the MixEmergency full screen output is at. I'll add an advanced option to the preferences to lower the window level, as I think that it would be best to keep the current level as the default (i.e. most people want the MixEmergency window on top of anything else that might pop-up on their desktop). The fix will be out in MixEmergency 1.2 - which isn't too far away now.