I just wanted to see if this is happening to other X-T3 owners. I've updated the firmware on my X-T3 from 1.0 -> 1.01 and now to 1.02.
Each firmware update has reset all settings back to factory default. That is, the "MY" menu settings get wiped, sound setup reset, screen setup reset, button/dial settings reset, ISO Auto Settings reset, AF-C Custom Settings reset, etc... BASICALLY a lot of work to redo stuff for each firmware update.
My X-T2 used to have this in the beginning and then Fuji figured out how to preserve settings between firmware revisions.
I just wanted to see if others are seeing the same X-T3 behavior before I try to get a bug report open.