Lovemybike, RU in clipless pedals?
One more knee pain idea...
If you just got clipless pedals, and your feet are fixed into a position that's not natural for you, that can cause knee pain. Maybe you need pedals with more "float," or, my bike shop guy tweaked my left cleat a few degrees because I am a little pigeon-toed on that side, and the pain instantly stopped.
One telling sign that your knee is in an awkward position is if one of your feet is occasionally clicking out of the pedal unintentionally. That was happening to me because I'd be unconsciously twisting my left heel out a bit more than the pedal could handle, and it would click free. Like I said, affixing the cleat just a few degrees twisted fixed it.
Good luck! I'm sure it's got to be one of these things mentioned here...