I'm a conductor and I can tell you a few things about intonation...
One, it is learned, period. There are genetic predispositions to being musically inclined, but you won't find anyone with perfect pitch who wasn't exposed to some fixed pitch instrument at an early age. Its no different than identifying shades of color with your sight, but you're doing it with sound instead. We only know a C is a C because we labeled it such. A440 is just that because we called it so. You only know red is red because someone told you it was, and you only know the difference between red and maroon because you've seen it enough to discern the subtle difference.
Two, it is a blessing to a soloist and a curse to an ensemble player. Instrumentalists do not play in absolute pitch, we play relative to the bottom of the chord which is present, otherwise even if we were all "in tune" it would sound like HELL. Thus, you're constantly evaluating where you should be playing pitch-wise and making minute adjustments to make things sound "in tune." To further complicate things, chord intonation is a fixed interval (DISTANCE), not a fixed pitch. The 5th of a chord is tuned slightly sharp, the 3rd slightly flat, so a G in a C Major chord is going to be slightly higher than a G in a Eb Major chord. And that's just two intervals, lots of chords are stacked far taller, especially in jazz and modern compositions. You can see how this would being to really screw with someone with perfect pitch.
Third, and this is the real kicker, even though there are fixed numbers that represent the number of vibrations per second in a note, those numbers don't apply to real pianos and organs. They tried that when those instruments were first invented, and they had to adjust the tension on the strings of the keyboard every time they changed keys. Not fun and completely impractical for a performance.
Thank GOD, J.S. Bach (Baroque composer) established a tuning series called "Equal Temperament" which makes each note equally "out of tune" from all the others so that every key is close to in tune. Remember the differences in chord tones I was talking about before? Apply that to 88 piano notes that span 144 Western scales and key signatures. It doesn't work, so they have to all be slightly out of tune so that you don't have to retune all the strings every time you change keys. Now before you get all concerned, no worries- you've been listening to it out of tune all your life and you've never noticed. Very few people can.
WHAT DOES THAT MEAN? That means the pitches that a young person learned their perfect pitch from are flawed, yet the sense develops nonetheless.
Quite a mystery, isn't it? =) That was more than most of you probably ever wanted to learn about intonation in music I bet *lol*