Clipless pedals cured my knee pain. I'd guess that yours are not adjustred correctly. There is fore/aft adjustment and angle adjustment. Most systems allow for a certain amount of float, that is, you can pivot your foot while clipped in instead of being locked into position. Assuming the cleats are adjusted right there is no reason it would be any different from riding on cage pedals. What position are you feet in on the cage pedals? Do you toes point in, out, or straight ahead? Is the ball of your foot centered over the pedal spindle (it seems obvious but my wife rides with her arches on the pedals )? You feet should be in the same position with the clipless system and you should be able to move you heels in or out a few degrees before the clip disengages and you clip out.