As Edwin suggested, what you're hearing is what the Buzz Feiten system is about. When you press down the string, you're stretching it by the amount of relief that's dialed into the neck, which makes the fretted notes a tiny bit sharp.
Part of the Feiten system is that the nut is moved closer to the bridge than expected. Doing this should be an overall improvement in intonation for fretted strings.
But this makes the open strings out of tune relative to the fretted ones. So the other part of the Feiten system is modified tuning that compensates for the nut position.
The last part of Feiten is how the intonation is set since everything is slightly adjusted. I don't know what's involved here.
These adjustments are tiny, something like 2-4 cents or hundredths of a semitone, so most people wouldn't notice them while playing, but if you use an electronic tuner, you're probably tuning your open strings closer than that already.
The amount of nut shift toward the bride is tiny - you can hear even the small adjustment in nut height in the tuning.
David Fung