Yes running the program on Windows/Mac makes a difference. Windows and Mac generally have different joystick input methods, so what setup works on one system may not work as well on the other (and vice versa).
Good to hear that Heli selection at least got it a bit closer.
I don't have any first hand experience of the Spektrum radios myself, but I believe it should be possible to remap the sticks to other output channels. Hopefully some other Spektrum owner will be able to help. Otherwise you might also try to search for an answer on the official FPV Freerider thread on RCGroups:
