Guys,,,greetings from Ireland, ive got a 2003 USA strat, white with rosewood neck, i tuned it up with the tuner then played an open chord D,tried a G and an A minor, the guitar would not tune up, barre chords were no better, i put on a new set of earnie ball 09's super slinkys, no dice, had the intonation done, no dice, the heavy E was even out of tune with itself, then i noticed that the pick ups were too high causing a magnetic pull on the strings which in turn gave a false reading on the tuner, so i lowered the pickups had the guitar intonated again and she tuned up perfect. i know this is elemental stuff but im an experienced guitar player and it never dawned on me that the pickups were too high, well you live and learn !

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12 guitars 2 hands not fair!

That's interesting. I have a similar problem on my MIM only on the #6 E-string. I'll have to try that later and see how it works.

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Don't worry, Be happy.

just take the pick ups down half way or so, tun up and see what happens.

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12 guitars 2 hands not fair!

Thanks for contributing with that tip! You never know what tip is going to work for your particular problem.