This problem is such a aggrevation... I seem to have to same problem but it only appears 80-90 miles in to a century and last for the rest of the day and maybe the next. I did some research after it last happened, and found the same thing that you were talking about...it's basically from high milage on your knees. I did talk to an "older" more experienced rider in my group about it one day and he suggested that I allow my clips to float as much as I could stand. This allowed me to change the position of my knee throughout the ride. Seems to have helped. If the pain is still there, see a sports trainer PT or someone of the sort, just to be sure. Hopefully is nothing serious. Then you will know for sure nothing is injured and you can find a way around the pain.