well i suffered so bad from coughing when running, and spitting up phlegm every five minutes. i used to have lots of catarrh anyway, but the running made it worse...
so, i found out that i had several allergies, i'm allergic to the moss (so it's worse when it gets wet) and several things in my diet.
i'm vegetarian, but became vegan earlier this year because of my allergies. running or any aerobic exercise can make any symptoms of allergies worsen, so you might consider a test. theyre about £20 and they do them in health food shops etc.
it could be that you've had some symptoms but the running made it worse. you dont have to cut out any suspect foods, though, the person who tests you gives you a re-introduction programme, but i enjoyed my nw diet so much that i never bothered with it!
it might not be that, but that's all i can think of. i hope you sort it, and good luck with your running!