Ever consider clipless pedals? Maybe something with a lot of float ... I find toe clips to be too rigid and they may be binding your foot in a position that your knee doesn't like.
Also, have someone check out your saddle position, it's usually more to blame. Perhaps you are too far forward in your saddle, so that when you are out of the toe clips your feet take a different position on the pedals than they do strapped on there. By tilting it back, you might fix everything (hint: bike fit ...).