I, too, have this problem on my X100F, which I returned to Fuji for repair. They replaced the lens and the main board to no avail, and are now saying this is a firmware issue. I understand that Fuji Japan knows about it, and is working on a fix, but there's no date for release yet.
(I first noticed the issue with Firmware 1.00; the upgrade to 1.01 made it worse. Indeed, it seems that some cameras that were OK with Firmware 1.00 showed the problem when upgraded to 1.01!)