Ideas
Having an issue with controllers and mouse/keyboard as well. I have a Razer Tartarus Pro (Keypad with a D-pad/Analog switch) so when I first loaded up the game the mouse worked fine in menus. Once in game though my aim drifted to the upper right, most likely Razer's subpar D-Pad has drift.
Solution: Unbind all controller bindings. Mouse now has priority since it's the only input bound.
Problem now is I like to fly on controller, so I use a Scuf Envision Pro Wireless. So now I have Gunner Aiming bound under controller (Right Stick) but also keyboard/mouse (Mouse Movement), but it doesn't react to mouse input. Bit of a bummer because when in land vehicles I can't aim with the mouse anymore. Really wish the game would just recognize both inputs or if there was a priority toggle for each group of control setting, i.e. Infantry, Aircraft, Helicopter, Gunner, etc. I get I might be on the fringe here with all my input devices.