Adjusting the intonation is an exercise in the art of compromise, the standard practice of matching the 12th fret harmonic and the 12 fret ( fretted ) note is OK, OK if you are going to only play open & 12th fret notes, but not much more than that, here's a few things to try, set your intonation like you have been, now with the tuner still plugged in, play some notes at the 2nd,3rd, 5th frets, play an open E major, then play an A major barre chord at the 5th fret, notice which strings are going out of tune, ( the worst ones anyhow) probaly the B&G strings will go sharp and thats whats driving you crazy, now here's where we have to compromise, you want to find the most acceptable setting of intonation and open string tuning, example,... play the B string at the 3rd fret, it's probaly #, so adjust the intonation so this note plays more in tune, play the open B, you may have to sharp or flat your open note tuning slightly, what you are working towards is the best you can get out of the fretted and open string tuning, Do you get what I'm talking about? It comes down to making it sound the best to your ear, the tuner is just a tool but your ear is the final judge, Work on a few strings and see if you can find the balance point, if you have anymore questions, just ask, Good Luck and Happy Tuning