This might or might not relate to your problem but the G (third) string is prone to intonation problems due to its greater thickness and hence its greater stiffness (perhaps others will correct me if I am wrong). This is why many luthiers build in compensation at the saddle, which alleviates the issue higher up the fingerboard. But there can also be similar issues at the nut end of the fretboard and compensated nuts exist as well, though I have never used one or seen one in the flesh. (Luthiers can also employ saddle compensation on the other strings, but it is most significant on the G string.)
However, not having any compensation at all on some of my guitars, I find that using a carbon G string significantly reduces the issue with the G string, presumably because it is thinner and more flexible than a nylon G string. It also can eliminate the "tubby" sound that the G string can have on some guitars. - Worth a try.
Last edited by JohnB on Wed Dec 27, 2017 6:01 pm, edited 7 times in total.
Hermanos Conde 1968, Stephen Frith 2007 "Guijoso", Christopher Dean 2018, Ana Maria Espinosa 2014