The old "standard wisdom" is that pain in the front of the knee, the kneecap area, may be caused by having the saddle too low and/or too far forward. Essentially, you are "hyperflexing" the knee. This leads to over-use syndromes similar to carpal tunnel.
Of course, that's only one possibility, a proper diagnosis (hopefully from a sports-medicine ortho physician) would be best.

Check out some articles on how to properly adjust your saddle for proper knee health in the meantime.