That is the issue. It shouldn't happen. It wouldn't be any different from the ball catching on fire as it arrives to the plate. It has no basis in reality, or science. A high pitch travels at exactly the same speed as a low one. If you really want to be technical, the lower pitch should be faster (for overhand or 3/4's deliveries) because you have a later release and thus a higher exit velocity .
Source:
http://pitchingprofessor.com/article...pitch_low.html
I'll find more sources in a few, but there's also a mathematical basis to it. You can imagine a triangle, where the base is perpendicular to home plate, and the opposite corner is the pitcher. The trajectory of a high fastball would be the adjacent side, while the low fastball, the hypotenuse.
The high fastball
seems like it's faster, in actuality, only because a high pitch has a shorter trajectory to home plate. The lower pitch, the hypotenuse, has a longer path to travel, thus giving the batter more time to react. Both pitches travel at the same speed, though.