If you are being asked to re-do all settings when starting MSFS then alas you are not alone.
This thread details many experiencing the same issue: UI broken and reset user settings
If, however, you are just being asked to reassign peripheral settings (e.g. joysticks/throttles) then this may be a slightly different issue.
Can you confirm if the first screen you see is “Accessibility Settings” when you start MSFS? If so then you are subject to the same issue mentioned in the thread I linked.