If you're using clipless pedals, do adjust the 'float'. As you can see, when you walk, your feet isn't perfectly straight (pointing forward), it's angled to the sides. So when you are pedaling on a bike and locked in with shoes/pedals, if your toes aren't in the naturally arced position, it'll put a lot of strain on your knees.

You might also be mashing too hard on a gear that you aren't ready for. You should have around a 80-90 RPM when pedaling, any slower and you are putting a lot of strain on your knees. So use those gears that you paid for!

If neither of the two above are your problems, then try KOPS. http://sheldonbrown.com/kops.html

And if all fails, hope to God that your professional fitter knows what he is doing and is able to alleviate the problem. Resting/icing will not help in the long run because you'll just develop the pain again and this might develop to be a huge problem down the road.