Maybe the AudioFX window was moved off of your main monitor? You can sometimes get into that kind of trouble if you install the AJA driver that makes the AJA hardware look like an extra Mac display. Try turning off the "remember window positions" pref, or trash your Media 100 prefs.
Thanks Dave I'll try that. Also I can't render fast motion anymore - so to get around that problem I booted into snow lpard where M100 ver 1.51 resides, only problem there is when you open a bin (from a ver 13project.) - you get no bin - what year is it again?