Have you tried uninstalling the Control Manager? I know someone will take my head off for this, but people have had problems with it and AH. Not everyone. Its fans seem somewhat rabid. But it cant hurt to try uninstalling the program and calibrating controllers with out the CM. If you uninstall it, calibrate, start AH and calibrate, and still have problems then you know its not the CM software. I know its tedious, but sometimes eliminating one thing at a time is the only way to find the problem.
Something else you can check, make sure that in the AH control mapping setup that each axis is properly matched to the right controller. Make sure your X or Y axis isnt mapped to the mouse or something silly like that. Roll -> X axis -> Joystick Pitch -> Y axis -> Joystick Rudder -> Z axis -> Joystick etc. If the mapping is off it could cause that but look fine in calibration.