intonation problems 1983 strat

I have an American made Strat from 1983? Anyway, after setting the intonation, every thing sounds great except a fretted D on the B string. When I check it against the tuner, it is sharp and is out when played against the open D string.

However, the B string itself when checking the intonation is good, as is the open D string.

Can this be a problem with the truss rod? Is this to be expected? Is this normal?

Any thoughts? Appreciate any help....

As each string on a strat bridge has individual action adjustment ( string height ) - i suspect that the height of the 'B' string is set too low and giving you a false reading ( touching another fret ? )
Try raising the action on the ' B string '

If that doesn't do it, you may want to get the truss rod adjusted.

you may be simply fretting the string too hard - sometimes the fenders have frets that when a string is fretted with a death grip it can affect the tone of your note.