Try intonating with a decent tuner by matching the fretted notes the 2nd and 14th fret. This should get all *fretted* notes reasonably close.
If after doing this you notice that the open strings are off in relation to fretted notes, it would indicate a nut placement problem. If this were the case, it would explain why the standard 12th fret harmonic intonation
method doesn't work for you.