I ran the same setup with no issues.  You have to disable the twisty stick rudder settings, then enable the pedals.  As a matter of fact, I run a X52 stick, and CH throttle and pedals.  I hope Santa will bring me a CH stick for xmas, but it's working fine right now.  
If you see me ingame I will be glad to help you with setup.  I fly as AKMeathd...