Make sure in the controller box above the joystick buttons, saitek pro flight x-55 stick is listed and not the throttle. I just tested this to see if that would cause your issue and it did for me.
Thanks a lot!
I was already going nuts as I´ve always selected the controller which I wanted to configure - once I´ve selected the X-55 stick as suggested by you it worked out for me and I was finally able to set up the throttle the right way.