June, 2016 - I still see problems with the Sidewinder Force Feedback Pro 2 and 'neutral'. When in neutral the roll and yaw are hard-left and pitch hard-down. I've noticed that if I install the Fly By Wire mod and I hover my mouse into any open panel of that mod, my neutral space is fixed! I don't know if that helps figure out what is wrong with KSP, but this joystick is still perfect and I use it in other games without a problem.
Luckily, I have a multiple monitor setup and I can just scroll my mouse off the screen and get the same neutral position fix. However, you cannot access any of the UI