Three possible things come to mind:
1) Atypical chest pain. I know, your thinking "WTF, I'm in elite shape. No way" But, stranger things have happened, and I've delt with healthy 19 y/o males that have had massive myocardial infarctions, but thought it was pain from a pulled muscle or old injury. Something to keep in mind.
2) Referred pain from a diaphramatic cramp. I get this in my left shoulder doing the exact same thing.
3) Referred pain from your liver. Doing a lot of bouncing around (ie, running) puts stress on your falciform ligament; this ligament runs directly down the middle of your liver, and running puts a type of "shearing" force upon it.