Manoeuvrability for me is Average, Fly Speed 20. My manoeuvrability becomes Perfect, Fly Speed 35 when I add Strong Wings as a Temporary Bonus. I add a -2 Flight Manoeuvrability temporary bonus to take the manoeuvrability down to Average but the speed remains 35
Also, I noticed that you can add +/- Walk speed under Feats&Abilities/Misc. Could you do the same thing with Fly Speed to deal with this?