My own design plane with ArduPilot 2.1 (no z-sensor, no shield) has a problem with it's aileron control reversed. Now let me explain: the ailerons work correctly with AP switched off i.e. normal flight (lets call this A), they also work correctly during navigation to the waypoints i.e. under the control of the AP (and this B).
However, when in navigation mode and using the Tx's stick to override the controls then the movement is reversed (C), i.e. if I push the stick right, the left aileron lifts...(btw the elevator, which is not set in the code to be reversed works fine all the time!)
Roll had to be reversed because of the way my servos are set up, if I reverse the roll in 1) or 2) above then A and B are reversed but C is correct, however of course, I can't fly like this.
Is your UAV a V-tail or Delta ??? I would like to set up a Stryker V3 but, no time yet
This mode is called Fly_By_Wire mode (stabilization with manual override). So change item #2-5 to 1 or -1 to reverse rudder/ailerons for this mode only
//2-5
#define REV_FLY_BY_WIRE_CH1 -1 //-1 will invert it // change to 1 or -1 to reverse rudder/ailerons
//2-6
#define REV_FLY_BY_WIRE_CH2 -1 //-1 will invert it // change to 1 or -1 to reverse elevator