that's very strange. it's a topmost window... UNLESS you set your wows to be topmost as well... if so, uncheck the topmost on the commands (or just move the override window over a non-topmost wow window)

btw... go to keyclone/setup/override settings and CHECK the audio-reminder (set the time to 20 seconds or so)... this has saved my bacon a few times. it'll make a noise (which you can change) to let you know override is on.