This issue presented itself during the beta and has recently reared it's ugly head.
The general idea is that the inputs from controllers such as xbox gamepads or joysticks are halved or not as responsive as they inputs on the keyboard.
The best example of this is switching off between controller and keyboard for each cyclic and rudder movement. The problem becomes very apparent.
See below for similar issues and for more description of the problem. This problem has not been resolved in the current version. Thanks to the Devs!
http://feedback.arma3.com/view.php?id=8002
http://feedback.arma3.com/view.php?id=2015 (where it was listed as resolved)