Thank you for all the replies. I took all your advice and tinkered with my bike this morning. I've now got my bike setup like a dream. My saddle was tilting back to much and my cleats are now more over the balls of my feet. I did all of these adjustments and no more knee pain. I'm going to carry my trsut park tool with me next week just in case I need to do any fine tuning. But hopefully that will be the end of my knee pain.

Danny