For starters you shouldn't be checking your intonation with a harmonic. Always fret at the 12th fret.
Check the distance from the nut to the 12fret whatever that is then double it that's the scale lenght. Then check the bridge saddles for rough distance the tune to open. Then fret the 12th and check for sharp or flat the intonat. Then retune and check again. So on and so forth.
Dave