Skuzzy, I had the same problem this morning. My post from a different forum.
Last night I spent a lot of time offline remapping my joystick/throttle and rudder pedals. I got them as far as I could and figured with the soon to be released patch and reading the forums I would be able to get make most of the settings I had prior to the new version.
This morning I went offline again just to check things out and the mapping I had for using my joystick to move GV turrets had gone back to NOT ASSIGNED. When I clicked on modify to map them again, the only radial button I can select is Radio 1. I am trying to set a Y and Z axis, not a button.
Is there a problem with the way the settings are saved now?
And now I've just had to remap by joystick settings for flight mode too. They disappeared as well.