This article goes into some not-so-common causes of issues with just one or two strings. Worth a look
https://www.guitaranswerguy.com/guitar-string-wont-intonate/
I am sure many know that some folks intonate guitars by playing an open string and the 12th fret harmonic, while some match the open string to a fretted 12th fret.
One rational I have seen for a fretted 12th note preference is that since that is how you will be playing, that is how it should...
I was adjusting the tailpiece on my new LPs, and following some advice originally made aware to me by DonP, setting the break angle at the same angle as that at the nut.
I began to do a little investigating about the effect of different tailpiece heights. There is a lot of BS out there.
Someone...