A string doesn't note true

[GTison]

I can't figure this out. I can tune it open then fret it and it's out of tune. I got a set of magnifiers and looked at the nut and the saddle I can't tell any difference by looking with the lenses. I've changed strings so it's not that It's been doing this for several months.
Frets are seemingly good, was re-fretted 2 years ago w/ larger frets. It's an '02 Fern Gibson.

Any EXPERIENCED Voices out there?

[RevJB]

Have you tried readjusting the bridge position?

[seanonabutton]

another issue is if you're using a wound a string... just a thought?

[sunburst]

Is it just one string of a pair, so the pair goes out of tune with one another when fretted? Does the offending string go sharp or flat when fretted? Is it the same at all frets? Which string is it?

[GTison]

I should have used "quote" marks. It's the " A " strings . I'll check today to see which one is going sharp of flat and post that. The A string is plain steel.

[GTison]

It seems that the first " A " string notes fairly true, but the 2nd "A" string notes approximately 3 cents sharp. It is difficult to tell with decay etc. but that seems about right. The E string and the rest seem closer than that.

[acousticphd]

It's somewhat important to know where you're fretting when you do the intonation test, as John was asking. #It is ~impossible for each string to be in tune everywhere on the fingerboard, and if I remember this correctly from past discussions, the unwound A strings will tend to intonate slightly sharp when fretted around the 5th fret, even when they are correct at the octave. # If a string is not bearing right at the end of the nut slot, that can make it note significantly sharp on the lower frets. #

Is the bridge/saddle significantly slanted across the top? #If it is, then the compensation of the two A strings may be different enough to cause the shorter string to be sharp when fretted higher up the fingerboard, like at the octave. #I would file the A string saddle so that both strings pass over it with the same length, and check the intonation again.

[sunburst]

I suspect the nut.
Look again at the nut slots under magnification and see that each string bears right at the front edge of the nut. If the sharp string slot has a chip at the edge of the nut, some crud in the slot, if it doesn't ramp back toward the tuner properly so that there is a "hump" in the ramp, anything that would make the sharp string longer, that would be the problem.
If one string is longer than the other, it will be under higher tension when the two strings are tuned together, but when you fret the strings they are suddenly the same length, yet one is still under more tension, so it notes sharp.
Also, check to see that both strings are the same height above the frets in their nut slots. If one is higher it will pull sharp when you fret the strings.

If, on the other hand, the nut checks out OK and it turns out to be the bridge, it's the other way around. The short string will be the sharp one. There again, both strings need to bear on the bridge the same distance from the nut whether that be the front edge or not. I still think it's more likely the nut, but if it turns out to be the bridge you can file the bridge slot so that the shorter string is the same length as the other.

You can forget about the frets, the problem is not there or it would show up on both strings.