Hi, GuitarCanuck.
Age of strings: As strings get older, they get very difficult to tune because they flatten out where they keep hitting the frets. New strings are nice and round in cross-section and ring true. So, if your strings are old, that may be the problem.
Tuners: Guitars are never really in perfect tune, they can't be. It's just the nature of the instrument, so you'll never get perfect read-outs from an electronic tuner as you test out various positions for the same note. Tuning guitars is always a compromise.
Intonation: each string has its own ideal length, which is why bridge saddles are set in at an angle and electric guitars have little adjustment screws down at the bridge to tweak each string individually. Cheap guitars are often lacking in this department.
Action: the higher off the fretboard the strings are, the more descrepancy there is between the open string notes and fretted notes, and that becomes more and more pronounced as you move up the fretboard.
That's all I can think of!
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