Not sure if this is an issue or noit, but let's get it out of the way.
The latest version of aquasuite is
2015-4... upgrade to it and check all firmware are updated for it.
Edit:
Edit: I can modify the fan speed (including the ones connected to the PowerAdjust 2 Ultra) in the 'Controllers' section in Aquasuite 2015-1. I guess its where it is supposed to be done!
I believe that is correct.