So I deleted the 1.41 mod and installed the updated one (in the correct location.) The in game icon is saying it's the 2.0 version, it sounds different. But I kept my joystick key binds which shouldn't have happened. I also lose the ability to map my pedals or throttle to an axis (like wheel brakes, throttle or rudder). They have red exclamation marks in those rows. No problem with other modules.
Any ideas? I attempted deleting reinstalling the mod and tried some stuff on the controls page. Love this mod, so if there's any devs reading this Thanks.