Neither elevation nor humidity should affect muzzle velocity, which is a product of solely interior ballistics. My first thought is that I wouldn't trust a Chrony as far as I could heave it. My second thought is the suspicion that you fired only three- or five-shot groups -- not enough for any meaningful comparison. If you fire ten rounds, then fire another ten rounds of the same consistent load, you're likely to find their averages different, anyway.
I also suspect that your chronograph wasn't exactly the same distance from the muzzle in both series of tests. A few feet closer to the muzzle, velocities are higher, of course.
