I had exactly the same problem recently. Hurt like hell when i tried to even shift my weight from one leg to the other, could hardly walk at times, never mind run.
I went to see a physiotherapist and he pushed and pulled in all the right places and he seems to have done the trick, after 3 sessions.
My SI joint was causing a knock on effect that my pelvis was crooked and was making one leg appear shorter than the other!!
Physio gave me some excersies to do, to strengthen and stabilise the pelvic area, and seems to have done the trick.
I would say, either go back to the Ostiopath or get a second opinion from a sports physiothrapist. but then everyone's different, but that's what worked for me.