Chondromalacia. Google it. The most common cycling RSI. Your saddle is not too high. The usual recommendation is to raise your saddle another 5mm, back off on the hard leg efforts. The best thing is to ride rollers about 30 minutes/day until the pain goes away. I'd also recommend in your case pedaling with your feet pointing straight forward if you are pedaling toes out now. Also see: http://www.bikeforums.net/training-n...l#post16081392
although in your case, it's the VMO that's too strong. It's the other way for most folks.

Stretching might help, too. http://www.bikeforums.net/road-cycli...l#post15372967