First thing to consider is all the above issues that may be causing the problems. Secondly, taking the instrument to a reputable experienced luthier for inspection and checking on a strobe tuner will reveal alot. Some players have more sensitivity to the compromises in the equal tempered scale to which you must explain to them the compromises of fretted instruments to which they just have to "get over it" ! Having every single note in perfect tune is beyond the abilities of equal tempered instruments, so dont even look for it. Most do not even hear the subtle differences in pitch in such a pronounced way that we listen in agony. If you think your instrument plays in perfect tune at every fret then check each individual note on the tuner, you will soon believe different !
The most common "upgrades" to improve intonation are compensated saddles and nuts. This allows tweaking of the individual strings length and minimize some of the main trouble spots. The best luthiers that work on vintage or collectible instruments use and install the Earvana compensated nut as they do not require the fingerboard to be shortened and are completely reversible. Also a capo can be used with them and there is no special tuning offsets needed. The most obvious improvement is better harmony of 1st to 3rd position chords.
It always amazes me to play an instrument that has terrible intonation to which the owner says they`ve never noticed ! This supports my belief that some players say they dont hear any improvement while others do. Another popular intonation compensation method, though far more expensive is the Buzz Feiten Tuning system. Before you make that investment I would suggest playing an instrument that has that alteration to see if you can hear the benefit. There is a list of authorized retrofitters found on their website.
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