You might have Ehler Danlos syndrome, my friend has that, it's extremely painful for him. You might want to check into that to see if you got it.
You do run, so I'm assuming the muscles aren't really really weak then. They could be, though, I'm not sure. I was gonna suggest possibly strengthening your quadriceps muscle, some people with knee problems, when they strengthen the surrounding muscles, the problems go away, as the tendons and muscles get tighter. So you could either do leg presses, or do full out squats (squats are better, but harder, and harder on the knees if your body doesn't like them/you do them wrong) and see if things improve. My sister has weak knees, and her PT person made her basically walk with rubber hands connecting her feet, weird exercises like that.