Your knee problem may have to do with how much you ride and how you do it. This is just a suggestion-- I haven't seen how you ride and I'm not a professional, but how are you riding? Are you pushing a high ratio with a slower cadence? Do you spend most of the time in the big ring? Did you go from riding 5-6 hours a week to 10-12 without working up to it? Are you stretching?

Not to say that a proper fit isn't extremely important, but the fact that some guy fit you for 2 hours makes me suspect that he either did an extremely poor job or that you're not taking proper care of your knees.