Originally Posted by phughes

I believe your seat is too high. The back of your knee seems to accelerate at the bottom of the stroke, which means you basically lose control of the motion instead of being able to pedal smoothly throughout the circle. You are also toes down. That and feeling for your heel cup should fix you right up.

Keep in mind the trick of setting seat height at the bottom of the stroke is misleading. I set mine with the crank in line with the seat tube, which extends your leg more than with the pedal perpendicular to the floor.

I had mine set similar to yours when I first set up my touring bike. That resulted in and injured Achilles tendon. It was swollen and sore. After lowering the seat it has never been and issue since.