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Just bought a Jazzmaster American Professional II, love the feel and the sound. However I’m seeing what I think is a strange anomaly. Tuned and intonated the guitar with a Peterson strobo plus and both settings seem to be right on the money. Then checked specs, neck bow needed a slight adjustment to get it to Fender factory specs, was about 0.018. Brought it down to 0.012. Retune but the same anomaly. I seem to get sour chords involving the 4th and 2nd string. Other chords seem ok but this just seems weird. String height at the first nut seems way high to me, could that be the issue? Around 0.020-0.018. Any help would be appreciated. Need to make a decision to keep or return.

Change the strings, if you haven't. Factory strings are often terrible, for reasons I can't fathom. An extra dollar to have the "speaking" part of the instrument sounding its best? Nah, just throw some no-name 9s on it.
But yeah, dud strings happen, and cause sour off-tones.
(edit) missed your comment about the nut but that would most definitely be a cause. if you fret each string at the third, you should be able to tap the part between the nut and the second fret, and hear a click on the first fret, but the gap there should be almost impossible to see. If you can see a gap the nut slots need to be deeper and that's the cause of your problem.

Thanks will do

Yep, nut slots/nut action.

Suggest measuring based on:
Checking Nut Action - frets.com

If it's anywhere near .018" it's way too much. I cut nut slots low enough that when assessing nut action the strings are so close to touching you can't really even see the gap.

Yeah checking the string height at 1st when holding at the third fret is 0.012 low E .01 high e.
That seems high to me.
Thx
B

Yeah nut slots may be responsible, and easy to fix, but beyond that I'd run a humble fret rocker up and down the neck to see that there are no high or low frets.

I put a set of brand new Daddario strings on and it’s even more sour that before. After a more thorough inspection I found two very high frets in addition to the excessive nut height.
I’m returning this one….

Good decision I think. Why fix their quality control issues for free?
These days with CNC necks etc, the next one will very likely feel exactly the same but without the defects.