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I was checking the intonation on a new guitar I just received. All strings intonate well when checking using the 12th fret harmonic and then fretting the 12th on the same string. On the treble "B" string, though it is correct up to the 12th fret, when I play above the 12th fret it plays flat.
Is that a saddle compensation issue?
I thought if the intonation was off it would show when checking the 12th fret harmonic against the 12th fret fretted note.

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Accoustic or electric?
My apology for not specifying. It's an acoustic.
First thing I would do is replace the string. It's suspicious that only one string in one area is affected; a saddle issue would affect the string along its whole length.
Hi Greg. I was thinking of doing that as well but I thought it unlikely that a plain string would be defective in a way to create a flat note. I will do it nonetheless and if that didn't take care of it then I figured I'd change the saddle next because with the other strings all in and the intonation being on it has to be the saddle compensation or the string I would think. It was mentioned by someone else that maybe the notes preceding the 12th fret are out as wel but just not enough to hear.
How flat is it? Can you pick it up by ear or do you need a tuner to indicate the flatness.
Personally it doesn't sound like a problem at all, it's just a minor imperfection, which about all fretted stringed instruments have.
If the B string is compensated at the saddle(they are normally set toward the bridge side of saddle) I'd put in a straight, non compensated saddle, and see what happens. Otherwise, personally, I wouldn't worry about it

Jim
Update. Last night I "really" fine tuned the guitar and paid particular attention so that I did not automatically "sweeten" the B string. I say that because over the years I've just become accustomed to the sharp C# in an A chord or the sharp F# in the D chord and have tuned my ears to flatten the offending strings a bit to compensate for it. Anyway last night I tuned without any adjusting and when I do that the offending note is fine but of course the C# is sharp etc. etc. I still think the B could be compensated a little more though.
I think there is another page about intonation going here .I had a look to find out how piano tuners work and blow me down they only tune one note to begin with.Then all the rest is done by ear!So get hold of a player with a good ear rather than a gadget.--However--I tried a different way of tuning today.I checked all the octave notes to the "gadget",not harmonics just fingered and I feel as if it played the Bach a lot more in tune.I was never happy with isolated bass notes but today they were all good ones!Reminds me how I noticed a subtle improvement on the violin when I was extra fussy about tuning.Just tuning from the centre of the strings may be the clue
Hi , I'd say if your 1st pos'n A and D chords are out , you better look at the nut slots on the B and E strings . Its common for them to be not deep enuff , which sharpens the 1st few fretted notes . Make that G string as well , dang check em all ! Len
I have just seen a site(DOLMETSCH ONLINE PITCH TEMPERAMENT & TIMBRE),and this absolutely hammers the subject into the ground like a TENT PEG! It covers more than 500 years of study .guitars -organs -pianos-flutes ANYTHING.A chart of different temperaments (Run the bar down the screen to halfway).This list is about 24 screenfuls.Take your pick but with a good tuner you could get a decent idea of why we end up with a workable compromise.--This site showed me why guitar music is mainly composed or transcribed in about 5 favourite keys. C_G_D_F_and B' and no harm in that! If you are a Jazz player that improvises in all sorts of keys and want EQUAL temperament,it`s over there in the tall weeds. ENJOY!
If the intonation at the nut is set forward a bit too much,
there is a small overcompensation.

In combination with the string seated a little high in the nut
it could be that it sounds ok at lower frets, but reveal itself
higher up on the fretboard as somewhat flat..

Try a capo up on the top of the first fret and retest everything.
Just to see what happens to that b-string.

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