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based on that explanation, you should have the issue all over the fretboard. To me, I only really notice a bothersome issue on the major D chord. And sometimes it seems worse than others on the same guitar.
What places me outside the realm of most people is that I find myself the happiest with that chord if I adjust the high E, rather than the B. I don't do this in general though because it messes up other chords, like the major E.
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I think it does happen all over the fretboard, but our ears (or at least mine) don't notice it as much as we (they) do on specific strings at specific frets. It varies from guitar to guitar.
I too sometimes adjust the low E or the B depending on what key I'm playing in. The term I've heard for this is "sweetening" after tuning, which I first read about in a Norman Blake interview.
The aim of Tempered Tuning (see the Ryan link I posted earlier) is to do a little compromising on precise tuning to fool the ears into not hearing as much of the intonation. Some electronic tuners have this feature, which either slightly flats or sharpens the notes instead of tuning them true.
Intonation: the curse of stringed instruments.