I'm not sure if you're describing the same type of pain that I had, but I had to stop running at one point because one of my hips kept hurting. The pain was in the back and when it got really bad, I could actually feel my IT band "clicking" when I walked. If you've ever experienced that, you'll know what I mean!
My chiropractor is really into yoga and recommended the half pigeon pose to stretch it out and it helped so much that I'm running again and I don't need to go to the chiropractor, yay! This youtube video shows how to do this stretch: http://www.youtube.com/watch?v=dGKzSnvahAI
I do this stretch before I go running, usually only on the side that's tight. I don't know how the muscle imbalance started, but I'm glad that I found a way to stretch it out