There is a lot of variation along the board with each fret, the relief, the action, etc. (you can perform a plek but most shops don't provide this) seems like you will always fight an out of tune situation unless you standardize your method of intonation....I think I'm just talking out of turn and the best thing a person can do is tune and check the 12th then go along the neck and compare a few octaves to find the ones that are out, tunes these and then go back and check your 12th again to see if it's out of tune.