When you say the first fit worked, what was done? I would call the shop you had the fit with and explain the knee pain and situation. It could be as simple as a saddle height or cleat adjustment. I have a great LBS and after buying a bike and recent upgrades have had some tweaking for a new saddle. Ask them point blank if you can come in and if they can take a look will you be charged. Most LBS will help without charging you. No LBS wants a rider in pain!