From the description it sounds like maybe your pressing too hard? If everything is intonated perfectly... The first variable is the human one.
Now... My js24p up around the 17th fret has a very minor tuning problem due to the fret slot. It's legit out of tune due to an improperly cut fret slot. Perhaps that may be your issue. But with my situation I can see it on a tuner. It's perfectly in tune open, at the 12th fret octave... Everywhere else as well, But not at the 17th fret.
The only other thing I could think of is perhaps your nut is shimmed too high. This can cause intonation issues on frets closer to the nut because of how much tension is being added to the string as it is pressed, before you actually come in contact with the fret.
Last edited by JsXLine6; 10-11-2020 at 12:22 PM.