While your in the sim you can press: right ctrl + enter and see a display of your input settings that is helpfull for trimming. Maybe this will help you diagnose any problems that you may be having with your rudder. I use the Saitek Pro Rudder and mine works well. It may also be that the autopilot is taking over some of the rudder functions causing you to have strange movements. i.e you have turn to target turned on.
Slardy