Both of my legs do that, and my knee pain turned out to be due to an extremely tight IT band pulling the knee cap to the right (right knee). I was born with tibial torsion as well, so things don't quite fit together as they would in a normal knee. I went through just about every part on my bike I could before I turned to medicine to see how to fix my knee pain although I only endured it for a year before seeking help.

Right now what has worked for me is getting shorter crank arms (165mm, I am 5'8") to open up the knee and daily foam roller on my IT band to keep it loose after my PT beat the knots out of it You also need to make sure that your feet are under your knees as you pedal, and if spacers/extenders are needed to get your feet under your knees, it is worth a shot. My pedals I am still working with. I have Shimano 105's, and the return-to-center mechanism requires that you get your cleat rotation spot on as the pedal system will return you to that point repeatedly. I have the cleats as far back as they will go so that I don't end up being on my toes and causing my achilles to tighten up. If your knee is really sensitive at this time, I would not recommend a return-to-center style pedal, but something like a Speedplay system which gives you plenty of float while your knee recovers from the 3 years of abuse. The PT I saw works at a sports rehab facility, so it was some tough therapy. He would work over my IT band to the degree that I got bruises down the side of my right leg, and I had to do a lot of exercises to strengthen my glutes and hamstrings.