Are you sure the position of the cleat on your shoe is right? It is possible that the little bit of float you described is contributing to the problem, but it's also possible that has nothing to do with it. While some folks need their feet locked in place, my knees are much happier with totally free float pedals (I use Speedplay Frogs) - but we're all different.
Your knees shouldn't be sore at all... Did you have a fitting when you put the cleats on your shoes? If you didn't, I'd recommend that you do that. Of course at this point it also sounds like your knee needs some rest and possibly some treatment, maybe PT.
Good luck, and keep us posted!
--- Denise



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