I too have knee pains, but I found something that has helped immensely. My foot doctor even thought this was a good idea. Part of the problem may be the angle that your leg is put in using the clipless pedals. I use free-float Shimano SPD-SL road pedals so that helpes lower the torque you may put on your knee. I have started using the "Cleat Wedge." Made by the Kool Kover company, you can use these thin plastic wedges between your shoe and cleat. They can help to angle your foot so that the alignment between your foot and lower leg (through the ankle) is straighter. This in turn helped lower my knee pains dramatically. When you are using your platform pedals, my guess is that you're actually angling your foot a bit without thinking too much of it. These wedges are not expensive and have been a knee-saver for me. Here's the link to their site: http://www.koolkovers.us/thewedge.html
Good luck, I hope this helps!!

-CyclingCowboy