l found similar with my Nikon D700 - it boiled-down to timeout settings
which may not have been obvious from the beginning (and also LENR).
Auto Meter OFF Delay - if you have similar, set to No Limit.
Auto Bracketing set to AE only.
No Auto ISO - Native Value.
Auto Bracketing Mode - Flash/Aperture.
Wide Area DF Points - in my D700 this is set to 51 Points 3D tracking.
If these AF points are too specific, small changes might not be registered
as you bracket. And of course, no AF Timeouts - or set to them No Limit.
Hope this helps
~Jack T~