| Bad strings, or a bad set-up.
So, are you SETTING the intonation correctly? That means, you play the open string (or the 12th fret harmonic, if your strings are in good shape and clean those two notes WILL be an octave apart) and tune the string to your tuner. That's your reference pitch. Then play the fretted note at the 12th fret. If it's in tune with your tuner then your intonation is set pretty well.
If the other notes are out of tune noticably, then you have bad strings. Setting intonation assumes the strings are consistent mass over the length of the string. If there's bits of dead skin, stale beer reisdue, nicotine, chicken grease, etc. in the windings then the string isn't consistent and won't play in tune.
jte
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JTE
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"Without space, music is just noise piling up on itself." TRK
Lakland Owners' Club # 248
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