I got this answer from Torsten Hans on the IPACS Development team and it worked great
Hello,
a new line of USB GameCommander has slightly different hardware features. This can cause the problem you described with the current version of AeroFly. This can be easily fixed by changing a few lines in the MAIN.MCF file. This file is located in the CONFIG directory of AeroFly Professional. Open this file with a program like notepad.exe. Go to the last lines and look for:
usb_commander_min 0
usb_commander_max 21845
usb_commander_mul 3
Change this to
usb_commander_min 0
usb_commander_max 65500
usb_commander_mul 1
This should fix the problem.