I had knee problems a couple of years ago and discovered that I need a lot of float in my pedals. I went from the SPDs that came with my bike to SpeedPlay Frogs (I prefer mountain bike shoes for the off-the-bike comfort). Frogs have a whole lotsa float and my knee problem went bye-bye. Haven't had a peep of trouble since (knock on carbon). I assume that SpeedPlay road pedals have a similar amount of float.

Good luck! Boo hiss to knee pain.