There's got to be more to it then - My saitek X65f HOTAS has been working fine along with saitek rudder pedals.
I did notice when rebinding everything, that it looked like something got assigned to the pedal toe brakes which caused a constant yaw to the right. But this may have been caused by me accidentally stepping lightly on the toe brakes.
After rebinding everything else, I simply went back in and rebinded pedals again, and it switched to the pedals RZ axis just fine.
(Note: In my case the X65f stick and throttle only counts as one device, with the pedals being number 2 device)
ED is not detecting more than 2 input devices. For a lot of us, Input Device 3 is rudder pedals.