That certainly answer my question about why the aperture sharpness results were basically identical when I switched my D800E from Standard to Neutral. If FoCal is switching the camera to Standard every time, the results would be the same. I have been using Neutral for several weeks now because of its effect on the histograms. When I checked my camera a few days ago, it was set to Standard. FoCal must have set it to Standard and left it set that way...probably when one of the AF fine tuning procedures failed.
I feel better. I thought I was losing it...and had set it back to Standard by mistake.