Have you tried not stretching before you start, but spend 5 mins warming up with star jumps, squats, spot running, windmills? I've never stretched before a run as my legs can't take it, they ache like hell after a few minutes if I do. I stretch out afterwards, after a 10 min warm down.
Also, obviously have you checked over your shoes? Do you have over pronation and are running in neutral shoes? Heel warn down and making you stress the muscle in a certain way?