That is a wrong way to check tuning! Natural harmonic on 12th freat will ALWAYS be octave higher than open string pitch. To really check your intonation you should play string normally at 12th fret and ensure that it plays as close to octave higher than normal as possible. I've setup my intonation few days ago and can say tune-o-matic bridge allows to fix intonation by 15-25 cents, no more. OH! On the Ibanez page i found a "guide" and there they said i have to play the flaggeolett. I will check it wit the 12th fret... There is no difference. If i play the strings open it's (start on low e-string) 6E, 5A, 4D, 3G, 2B, 1E. On the 12th fret it's 1E, 5A, 4D, 3G, 2B, 1E and on the flaggeolett it's 1E, 5A, 4D, 3G, 2B, 1E aswell. I am so confused right now :D