Not sure it's with joystick, which is correctly calibrated in windows - Saitek ST290 Pro
But my 0 (zero) axis is mixed up with Axis 2.
Everything register correctly when setting up controls in menu.
But when in any plane. The throttle is controlled with both (Pitch and throttle - Axis 0 and Axis 2.
There may be an issue with the config file, please delete your iomap.cfg in the data dir and reconfigure.
Had this problem too, deleting iomap.cfg and reconfiguring solved it.
There's a bug(?) in external cameras, they behave differently than before, "third person follow" and "third person follow aligned" seems to be the same camera, with free camera pitch and roll axis (was attached to aircraft before).