Nut relief of 20 thou is a pretty common setting. I think it is a combination of measurements as suggested .
Also, do you have higher frets on this guitar than you are used to? As pushing down too hard when fretting will also make a note go sharp. Nut relief could come down to 18 thou by sanding off the bottom of the nut.
If the string is in tune open and 12 th fret then the intonation is correct. Suggesting the fretting of the note is pulling it sharp. You are no stranger to guitars, so perhaps there is something about this set up or technique on this one causing it...

How much neck relief do you have.: capo on first fret and fretted at body, how much height do you have above the 7 th fret?