Some things come easily, others need waaaaayyyyy more work. Sounds like the fine tuning of your fit might be one of those that needs lots of work. Did your bike fit include pedal adjustment? Pedals with more float might help. How is your cycling technique? Does the pain happen only on climbs? Are you a spinner or a masher? What about if you ride on your trainer with high tension? I agree with CorsairMac. Maybe you need to go back to the big fit and see if there is anything else they can correct.

Other than that, read your signature line over and over!