I believe you only see the extra pump, fan, flow meter e.t.c that you connect to your PA's in the aquasuite 2012 software & not the PA's themself's, You need to also have the latest version of the old aquasuite software used for the Aquaero 4. It's also from the older Aquasuite 4.69.00 that you can flash & update the PA's firmware to the 1003 version, but again this must be done through the older AQ4 Aquasuite software.
That was how I got mine sorted, just remember that you don't actually see the PA's in the Aquasuite 2012 software, only the Items that you connect to the PA's will show up as added Fans, Flow meters or whatever you connect to them. If you see what I mean

N.