Do you have the controller connected with a USB Hub? (recommended)
What do you see on the Radio Display (keyboard #2) when you move just the elevator stick does the rudder stick also move.?
Next type "joy.cpl" (less quotes) into the windows search box, select the controller and select properties, on the Test screen, move just the elevator stick and see if the rudder moves with it, also click on the Settings tab and select Calibrate, (follow on screen prompts).
Next go back to RF and calibrate and test the controller, if the controller is still malfunctioning then call technical support, hopefully your controller is still under warranty.