Same issues. 
Did not see your post, so unfortunately I have another post (merge all of them?). Not sure when this started. Maybe when i duplicated my settings and removed the earlier setting, OR its just beacuse of latest SU. But from what I can tell, its ONLY sensitivy settings thats not saved right (even though the spinning thing is…well, spinning). I also hade some question regarding sync from cloud or from local drive at one time.
Any solution so far? Check my other post and see if you can add something. A bug is reported regarding this problem, but I relly do find it to be a quite severe bug, and I certanly hope they will fix this ASAP.
https://forums.flightsimulator.com/t/joystick-settings-not-saved-any-longer/504037/4