Without examining him I can only throw out some thoughts. I would want to know whent his started, how often it happens, anything that makes it better etc. I would want to see what shape his foot is, watch him walk and run, see what shoes he wears, what he plays etc. If he has some ongoing trauma, I would think he would hurt while going through various activites, not when at rest.
I would question about his diet- getting enough calcium, magnesium, vitamins.