How is the action set - what gap is there between the 12th fret & the underside of the strings? The higher the action, the more the string has to move, from open/harmonic to fretted, the more tension is changed & the more difficult it is to set the intonation. Also make sure you're not pressing the string 'behind the fret' as you might when playing, just the most gentle touch to hold the string directly onto the fret is all you need.
Also - what tuner are you using?
Apologies if you know all this already, I'm guessing not?
Cheerz, john