The most common response to this question is usually to check cleat position or change to pedals with a different float system (eg speedplays). However, if you pronate significantly (as you indicate) the knee pain might also result from your legs/knees being misaligned through the pedal stroke. If so, this can be corrected in a number of ways - custom orthotics, angled pedals (Look CX-7 are the only ones I'm aware of), Lemond wedges under between shoes and cleat, or Specialized body geometry shoes all provide a way of placing the foot at a slight angle on the pedal (ie the inside of the foot is 1-3 mm higher than the outside). I also pronate significantly and experienced knee pain, which only went away after I started using the -3 degree angle CX-7 pedals. Lemond wedges would be least expensive way of testing this; the Specialized shoes are also very nice if you happen to need a new pair of shoes (both Lemond and Specialized have good explanations of these issues on their websites).

Of course, it could also be some other problem (possibly just adapting to the new position after changing the pedals). See if you can find a competent physiotherapist or sports medicine professional with cycling experience or a fit expert, although in my experience most "experts" are largely useless and the only real solutions have come from personal trial and error over a long period of time.