Hi Cycling
i can relate to your knee pain. I have right knee problems and here are some suggestions:
1) make sure your seat height and fore/aft position has been done correctly
2) it IS possible the cleat isn't set up properly on your shoe. Your clip in position should follow your leg "bends". that is, if your knees point in then the clips should be pointed in a bit.
3) another possibility is trying another type of pedals, i have heard that Speedplay pedals are a lot nicer for sore knees.
4) you may have a weak right knee. have someone watch your pedalling, does your right knee "fall in" on your down stroke? this will probably also happen if you try doing squats. what it means is that your muscles around the knee are weak, and you need to do some exercises to strengthen them (this is what my boyfriend had to do).
hope some of these ideas help.
happy riding
Han