That's a puzzler. Never even heard it mentioned before.
It seems you have had it "working" for a while.
I use a joystick . WOWP automatically sets my Axis. (X Y Z).
When you first enter the hanger, hit the "esc" button, select "settings" and the settings screen will Display. The "control scheme" slot (a dropdown) should be set to "Joystick". You will then shown the "axis" preset. Don't intercourse with it.
Modify your other settings if you wish. I can't think of a reason why you would need to change the Yaw, Pitch, Roll Defaults for a joystick. I've played WOWP since beta, with 2 different joystick manufacturers. But it's possible that they have "bettered" your experience with latest update.
I've never experienced this problem. 
I'll save you some time as well. After submitting a ticket WG will answer "soon". ©
They will ask you some dumb question, tell you to clear your cache, suggest that you are running mods and that you stop. None of that will work, but what the heck, clear your cache anyway, and then return to the forums and hope someone who isn't a brain dead stroked out old dude like me can actually help you. Good luck. 