Did they test/look for fluid & or inflammation in the pleural space? (the space between the lungs and the membrane that surrounds them). It can be difficult to see on chest films. Lungs look clear, but they have difficulty expanding to full size. It's particularly difficult with athletes, since they usually have larger than normal lungs. Even a pulmonologist can miss it on the films unless they're looking specifically for it.
With either fluid or inflammation in the pleural space ordinary breathing (esp for athletes whose lungs only need to inflate about 1/3 or LESS full for walking/brief -for them- exercise) can SEEM completely normal, as they don't need to actually inflate their lungs that much and DON'T on a day to day basis. But put them into training and they start using their lungs the way they've been "grown" to.
As a former athlete, even smoking and with pneumonia I have almost DOUBLE the lung function of most people. If I'm with a doctor who doesn't know that pudgy little me used to be half pro I have to insist on xrays when I know I have pneumonia (because I'm "blowing" above "normal" in the lung function tester). Each and every time, I'm right and I've got fluid blocking about 1/3 of MY NORMAL breathing space.
Now, your son doesn't have pneumonia... but he IS an athlete... which means that the docs need to be looking at his breathing issues through that lens.
I'm willing to lay money on the table he's got fluid or inflammation in the pleural space, since the problem is ONLY kicking in when he's using his lungs to their "full" potential, and that they're just not able to inflate fully because they're being blocked.
((aaargh, stupid computer crash... adding))
If NOT a pleural space issue... I'd think next toward atelectasis (partially collapsed lung). Also REALLY hard to diagnose in athletes because the lungs are so large. The doc (or you if you have a stethoscope) has to move the scope not just in the standard 4 quadrants to listen, but up to 20 different places on EACH lung. Doesn't usually show up on xrays, although it can. It "sounds" like silence, and can be as small an area as a grape or as large as half a lung or more. My son currently has 6 areas of atelectasis on his right lung right now and has had more than 10 (and he's just an 8yo). Again, it wouldn't interfere with your son's normal activities, but would DEFINITELY show up as he's trying to be athletic and NEEDS to move air through the collapsed area and can't.
In any event, as an athlete, he's going to pass normal tests with flying colors. Take him to a pulmonologist (obviously) and make sure you pound in ATHLETE, ATHLETE, ATHLETE, into their heads several times... since he's going to need to be tested under THAT lens, rather than 'normal kid' lens.