Possibly it may be worth you trying an aftermarket Earvana for example.
1-5/8" (1.658") E-E 1.340" Fits 12" to 14" radius 1-11/16" (1.689") E-E 1.395" Fits 12" to 14"radius Gibson and Acoustic style shelf nuts 1-11/16" are 3/16" thick at the base and 1/4" tall from the bottom of the nut to the top of the fret board.
earvana.com
Have you also tried verifying that the measurements between the nut slot and the 1st fret are correct for the scale length?
www.stewmac.com
All of the above said, guitar necks can never be fully in tune everywhere, especially with chords, so most tuning is a compromise.