Cleats that force your foot to rotate slightly from its optimal position can definitely cause knee pain. Angular float is a good thing, and you may have had more of it with toeclips than with your current clipless system.
Pop on over to amazon.com or ebay.com and order yourself a copy of "Save Your Knees," by James Fox, M.D., the official orthopedic surgeon of the 1984 Olympics.
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"Far and away the best prize that life offers is the chance to work hard at work worth doing." --Theodore Roosevelt
Capo: 1959 Modell Campagnolo, S/N 40324; 1960 Sieger (2), S/N 42624, 42597
Carlton: 1962 Franco Suisse, S/N K7911
Peugeot: 1970 UO-8, S/N 0010468
Bianchi: 1982 Campione d'Italia, S/N 1.M9914
Schwinn: 1988 Project KOM-10, S/N F804069