One other thought, what lens are you using? And do you have a different lens? Just thinking out loud, there may be some issue with the installed lens. Fuji glass is much more electronically controlled than any other camera I have ever used.
My 35mm F 2.0 AF motor started to fail, and it created total havoc on the X-T1 and X-Pro2, all kinds of strange things. Fuji replaced the motor and no issues since.
Paul C