believe it or not I had the same issue.....
What did I do to resolve it?
Well what I was doing was pressing my knee against the Desk leg while sitting, not sure why but I was doing it. So basically I was just pushing my knee into a metal bar subconciously, once I learned to stop doing that I've been fine. I know this is rare, but I never realized I been doing this.
also when I am dehydrated, my knees are the first thing to hurt, is he getting enough liquids?