I have the same issue. I included the steps I followed below.
1.
I customised the front dial to change aperture and set the lens to A.
I have the rear dial set to Shutter speed
Result:
Front dial won't change the aperature.
Rear dial will change shutter speed
2.
I then customise the front dial to change Shutter speed & Iso
I customised the back dial to change aperture
Result:
Front dial changes shutter speed, when I push the front dial in I can select the ISO, now the front dial changes the Iso
Rear dial won't change aperature
I tried this with two fuji lenses.