So I don't know when this started happening, but I never had this problem a few years back. I'm starting to recognize it more and more. I tune my guitar, according to the tuner, then I play a few chords. E, A, C, G, D. You know, the classic CAGED patterns. I hear something out of tune (most times the G and/or the B strings), tune it down or up till my ears are happy again and like the chord, I hit another one and I hear dissonance again! It's driving me crazy. I think my ears are refined enough by now to hear the imperfections in guitar tuning and the compromise, something I know the true temperament fret system fixes. But good luck affording a guitar with those weird frets or maintaining it. Anyway, I did a bit of research (remembering the name Buzz Feiten in the back of my head) and found this video: I will try this next time I intonate. Seems actually reasonable considering the G and B strings are the assholes in 99 percent of the cases. I took a screenshot of his piece of paper: So according to this you first intonate the G sharp and the B flat, then you tune em the other way around. The guitar in his video sounds quite in tune. Just thought I'd share. Opinions and your experiences are welcome!