Yeah, sounds like a setback issue to me. Where is your knee hurting? I get a very specific, instantly recognizable pain if I am too far forward -- a tendon that is centered and right above my kneecap. It can get quite painful, but if I stop and push the saddle back, it goes away immediately, during the same ride...

Watch out for anyone who tries to fit you on a bike that's too big for you by moving the seat forward to shorten your reach to the handlebars. They should always determine the right fore-aft saddle position and then fit your reach taking the saddle setback as a given.