I read an article were one of the Guitar World columnists said.His Les Paul tends to play a little sharp past certain point and he adjusted his intonation a little sharp to compensate.
Basicall maybe your guitar needs the G string set for an average over the fret board rather than the standard open and 12th fret method.Try messing with the intonation to see if you can get the whole fretboard within reasonable intonation.
(I've had a few beers so I hope that came out in understandable english)