quad pain during run

would anyone have an idea why would one quads hurt so bad during a run, here's my dilema when running a month and a half ago stretched my whole body for 15 minutes before my run after the 2 mile mark i just felt a sharp pain on my right quad i just had to completely stop, ended up seeing a doctor and i was told that i've strained my quad muscle, before that he asked me about my training,i train 5 days a week swim, spin, and run, then asked about my running shoes i told him it did not have not even 100 miles on them and i use inserts, well after all that i was told to lay off for ten days, well i did, actually more than 10 days but i kept my swimming training going and moderate spinning, no running, now here i go today stretched out for my run it was perfect weather have my music going and the breathing could not been better at a 4.5 to 5.0 pace first 2 miles went very well started my third with a 1/4 to go WHAM here comes the pain same right quad i finished my 3rd mile but i could not continue, if anyone has any and i mean any advice please let me know i need all the input because it's quite upsetting not getting through my runs and this has never happen to me before during my runs, now twice in a row, unreal.