Are his knees red just in the area that he has been kneeling on? If so, then thats not unusual. As this is happening on a daily basis though, I would take him back to the doctors and ask for it to be investigated. If the doctor refuses, demand to see another doctor for a second opinion. If he has a problem with his knees, joints, etc ( and that is a big if ) then it needs to be seen to now rather than later as leaving it can cause damage. Dont panic though, it simply be a phase he is going through whilst growing and will therefore grow out of it soon.
Dont let the doctor fob you off though, insist he gets seen and this is looked into properly. Make a noise if they refuse to do so!