I have seen the same behaviour with non-Nikon lenses. In my case an older Tamron f/2.8 and an older Sigma f/2.8 are perceived to be the same lens by the AF Adjust table. Nikon brand lenses are fine and are recognized uniquely.
So far, I have chosen to avoid the cost of sending the lenses back to the manufacturer for firmware updates.
If only one of your two lenses requires AF Adjustment, one possible workaround would be to turn off the AF Adjust unless it is required for the lens in use. Keeping the AF fine Tune item at the top of My Menu makes this option slightly less inconvenient.
The proper solution of course is to get the lenses updated by the manufacturer.