You say it's been modded - my first question would be what did you do to it?
Second question: compared to the 5th fret, do the 17th fret notes sound sharp or flat? Or do they just sound "off"? (You might want to use a tuner to determine this, unless your ears are really good)
Third question: does the 12th fret harmonic match the 12th fret fretted note? If not, which one sounds higher - the harmonic or the fretted note?
Q4: How old are your strings?
I'm not ruling out a twist in the neck, but without seeing it, I think there are other causes that are far more likely. Maybe we can narrow this down somewhat... some of the possible causes have simple solutions.
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