Originally Posted by Jeff Gray
I think a lot of knee pain around the patellar tendon is due to shin angle and not keeping the quad muscles active during a squat. Maybe try some box squats and see if you still get the pain, as they allow you to greatly reduce shin angle and make you sit back into the squat more. Just an idea.
Poor recruitment of the hamstrings (knees too far over toes -- not enough "sitting back") leading to some maltraction of the patella. Certainly a possibility.