I observed the same problems with X-PLANE 11. My solution:
I disabled the “Analog Input” to “Not Bound” in the CLS2sim software
In the X-PLANE settings you find the CLSErudder in joystick setting for your Rudder and Brakes.
I also adjust the sensitivity settings (aircraft dependent – for me ZIBO 737-800)
I would also mention the following:
Lately it has happened very, very,very often that you lose the connection between the CLS2sim software and X-plane. Very annoying, especially if you disconnect the AP and you want to take it over manually and nothing happens.
Jo va Bra