Same problem goob. Brand new CH combatstick with rudders(essential)and Pro throttle. I disabled the top right hat(too hard to reach)and made a different hat HAT 1. Pro throttle comes with configure program called speed keys with which you can set up your joystick also but no matter where I put HAT 2 it still registers as 7,8,9,10 buttons. The SELECT JOYSTICK button in calibration screen showed the proper joystick but I messed with it for hours unable to figure out what to do with it.
In the end I just set up 7,8,9,10 as the view I wanted and used the hat as is. I also made button 3 switch between stick 1 and stick 2 and changed my hat views in stick 2 so I have 8 defensive views and 8 offensive views.
Still would have been nice to figure out what they intended in Select Joystick screen.
Hope this helps!
Night