has it something to do that some controls are assigned to a keyboard function or an other controller? I had the same and I found out that my rudder pedals and and yoke were both connected to the same functions causing this problem.

I know the control settings are an huge list but you need to find the cause of the problems in here. I also have a CH Flight Sim yoke but don't have this issue. Also the issue can be in the calibration of the yoke. did you try to calibrate it and do you see strange behavior in the calibration dialog?
If so try to connect your yoke to the an usb port directly connected on the motherboard. You can find these usb ports at the back of computer.