Since AFMA is calculated using internal functions it technically shouldnt matter if you leave it on or take it off. I would take it off if it were me (I dont use filters on my lenses).
However you can also run a sharpness test with the pro version and it will cycle through every F stop and calculate the best Fstop for the sharpest image. Test with and without the filter to see how much your filter is affecting your images.
I am wondering when you do the microadjustment with FoCal do you leave your UV filter on or take it off. I presently using B&W XS Pro on my lenses.