I experience the exact same things you are Mandrix. Whenever I am adding an output to a controller, it shows me the dialog screen wiht the first AQ5's fans, and then after I click 'OK', it brings up another dialog box with the second AQ5's fans.
And at least 50% of the time when I make a change to any controller...the Aquasuite shuts down, freezes up, or drops its connections to the AQ5 units. Very frustrating. I'm using 2013-2 with an AQ5 XT and and AQ5 LT.