I’ve heard some guys say that not all strings intonate the same. Different string thickness, like coating or a thicker gauge could throw intonation off. Again just what I’ve read.
My guitar does what you describe and I think it needs the nut adjusted. If I tune the strings open, then fret the low E at the third fret it’s sharp. I think I’ve got it figured out now, some strings I have to tune a little flat and some I have to tune sharp to get it to sound right. It’s a pain though.
I think it’s either the nut or the saddle. This is my first guitar with a saddle that’s not compensated. I don’t know.
Is your action high at the nut?
They say you can check this by capoing the first fret, then tune the guitar and see if it sounds better making chords. Basically eliminating the nut. I’ll see if I can find that thread.
Here ya go:
acousticguitarforum.com/foru … p?t=259427