As Carl indicated, you're likely experiencing a compensation in the imperfect intonation of standard scale guitars. As you tune a string, it's usually in perfect tuning while being played open (at the nut). As you fret that string, the note may be flat or sharp ever so slightly along the scale of the neck. Depending on the guage of strings, the scale of the neck, the type of bridge... even the way that you play, you may experience different levels of the intonation on your guitar being slighlty off. Tuning an open string slightly sharp or slightly flat at the nut (open), can compensate for some of these oddities while playing the guitar.

More sensitive ears might be more intune (pun not intended) to this than most! So, it's a good sign that you have a keen ear. And if it sounds good, it ain't wrong.