They do. They have two sensors that detect a break in the light that are a known distance apart. The time taken to travel that distance can then be used to work out fps etc.
The blast of air somehow disturbs the sensors accurately picking up the pellet. Maybe tiny particles of debris like someone suggested on the BBS?
I've had it when testing where the chrono has given weird readings with the muzzle right up to the 1st sensor. When I move the muzzle a couple of feet away ( sometimes just a foot ) the chrono readings are normal.