Do you watch your knee while you pedal? Mine used to sway inside on the upstroke, and I had to concentrate on keeping it from doing that. Some things online I've read suggest it's a matter of conditioning the muscles to work correctly, while others suggest shims for the cleats. In the end, I decided to pay more attention to my form, and the knee pain vanished.
It might also be you have a build of bad humors in your blood and you need to bleed out some of the bile. In that case I recommend finding a trusted bloodletter (phlebotomist, wanna-be goth "vampire", or similar) and letting them disgorge you of bad humors.