I updated to 2.0.3 and now every time I open the card slot or turn the camera off for couple of seconds, it turns my AF micro adjustment setting to disabled. It still remembers the adjustment value, but is not using it any more.
Out of curiousity, do you have Orientation Linked AF Point set to 1: Select different AF points? I ask because the 1D X had a similar issue on firmware 1.0.2, which was corrected with 1.0.6.
Sorry, false alarm. It was just me being dumb. I was on C1, so every time I turned camera off and on it reloaded that setting from memory. On M it works as expected. I just got it from service after shutter/mirror replacement and they must have made some changes. I got confused because I also have 1D mark iv and there loading settings doesn't influence AF micro adjustment.