One of the more common problems with the knee is a problem with the ilio-tibial Band (ITB). It is on the outside of the upper leg wear the seam of the pants would be. It control knee mechanics especially the knee cap. It also influences what happens at the pelvis and the feet. The pain is usally behind or just to sides or above or below the knee cap. If this is the case you should try and release it by rolling it on a foam roller or by having Active Release Techniques done on it. You may also be suffering from pelvic instability. You could detect this by putting your hands on the tops of your ilaic crests (most people would call this the hip bone) and looking into a mirror and then lifting your leg into the air with the knee and hip at 90 degrees of bend. If you hands and hips dip down or up then you are unstable. This would indicate that every time you took a step or took a pedal stroke the pelvis, knee and foot would be doing some abnormal biomechanics which could be effecting the knee. This would best be corrected with Pilates