I had the same type of pain (kind of still do, but its not as bad) you are explaining. My physical therapist identified it as pain being caused due to the patella not tracking correctly. She explained to me that there are a ton of components that contribute to the proper functioning of the knee, and that since I hadn't really been using any of the muscles for three months they started to operated differently than how they normally do. She was insistent that if PT was done regularly and properly, that the pain would go away, and it did for me. I still feel the pain a little bit, but I surmise that is because I hardly do PT anymore. My affected leg is still noticeably smaller than it originally was, but I am able to do most things, including basketball, which was the cause of my tibial plateau fracture that eventually lead to two plates and nine screws to be inserted. I have noticed that the best exercise to help this particular issue is to stand on a step or a platform with your bad leg holding onto a handrail, and slowly lower yourself down until the heel of your good leg meets the floor, and then rise back up. I would do three sets of twenty reps 3-4 times a week, and eventually I would increase the height of the platform to get a more intense workout. I am 24, and my injury was sustained on May 2, 2011. Hardware is coming out in 5 days! Woohoooo! Good luck with the pain; its a bitch, but you will get thru it!