CostaFonix wrote:
just my 2 cents ? worth, I have found that some tuners are not as accurate as others,,,so choose a good quality tuner when setting your intonation. I also check the harmonic on the 12th fret as well as fretting the 12th fret (you can see a subtle difference). Other obvious things are ensuring the nut is clean (i.e. not choking the strings) and of course use new strings.....
Tuning and intonation are not related......you can tune your open E string (say) to
any note, BUT the corresponding note at the 12th fret should then sound
exactly one octave higher (to the ear). That is intonation. If it does not you have to adjust at the bridge. Also make sure your strings are in good condition because an old rusty and fatigued string will not "follow the rules".