Cause of right knee pain?

I'm a pretty serious runner (I run half marathons) and I also play basketball. About 6 weeks ago, I went running, and from the very beginning, I felt this sharp/pulling pain in the back of my knee. I've never had any problem with my knees before, so I'm not very familiar with knee injuries. My first thought was that I tweaked a tendon or ligament. I stayed off it and iced it but there hasn't been any improvement. I finally went to the doctor and they did a physical examination, and they said my symptoms sounded like a Baker's cyst, except they couldn't find it. They said that a small cyst wouldn't be giving me this much pain. It occasionally causes pain under my kneecap, and my knee feels inflamed all the time. When I plant my foot and twist my knee/thigh inwards (to the left), I feel a painful pull in the middle of my knee, and then sometimes it locks when I twist it back. I can do almost all activities (except running and extended walking) and my range of motion isn't really affected. Any ideas what it might be?