I just realized that I don't understand tuning. I've recently read that if the open strings are accurately tuned then the first few frets are typically sharp particularly on the G-string. It was a revelation! That sharp A on the second fret G-string was driving me nuts.
It is claimed that some people tune a little flat to and/or unconsciously adjust their fretting to compensate.
Then there are things like the Earvana nut & the Buzz Feiten System. It makes this guy