It's quite simple really. The guitar's intonation can never be precise. By construction there are bound to be irregularities up the neck, that is the way most players use a "tempered" tuning, mostly by ear.Originally Posted by tjcurtin1
Apart from that: What kind of tuner did you use? Also are you sure you applied an even pressure to the frets and used the same picking technique? Even a small difference goes a long way! Finally you must be sure you have a properly cut nut and fairly well dressed/polished frets.
Hope this helps.