I've had knee pain in the past, actually more like a feeling of "pressure" in the area of the knee, but it usually would happen hours after I did something strenuous. I came across some info here on BF about I.T. Band Syndrome (the I.T. Band runs from the lower back area to the knee area, and when it becomes tight it can cause discomfort to those areas and the areas between them). I experimented with stretching which brought immediate, if temporary, relief. What seemed to help the most was using a foam roller (you can often find these in the sporting goods section of a dept. store) to loosen up the I.T. Band. This might not be your problem but you might want to consider it and do some research.