Originally Posted by Terex
Occam's Razor : "when given two equally valid explanations for a phenomenon, one should embrace the less complicated formulation"
Adjust your seat, per other posters. Fiddle with it, a little at a time, and you should find a position in which your knee doesn't bother you. I had exactly the same problem when I first started riding. All the other "kneecapulitis" theories are much less likely.
All though I agree with the conclusion (try adjusting the seat), I do not agree that "kneecapulitis" theories are less likely. Actually I think there is most likely that they are the same animal; some kind of inflammatory response ("kneecapulitis") to over stressed body tissue, which could or could not be relieved by adjusting the seat.