having the same issue. Seems that maybe KSP just doesn't support more than 2 devices at once for some reason?
Saitek pedals, CH Pro Throttle, CH Fighterstick, here. Pedals and throttle work, stick does not. The stick is recognized in game as "joystick 2" pedals as 0, throttle as one. I wonder if, for everyone else here, the one that's not working is recognized as 'joystick 2'
I really don't want to use the CH manager to merge these into a single stick to get over the axis limit. That's a huge pain, and messes with all my other applications. A fix coming soon, I hope?