Believe it or not, this is quite common and from what I understand realitively normal for a guitar to "flatten" as you move up the frets. I have a Godin electric I have had setup 3 times and had 2 new nuts made for it for this same problem and at the same time, my g string seems sharp after the 3rd fret. The guitar techs who did the work told me of an old saying, "guitar players spend half their time tuning their guitars and the other half playing out of tune."