It sounds just like what my son had even worse when he was your son's age (he's 27 now.) He had all his vaccinations. I took him to the pediatrician. I remember her saying that we had to be like detectives, noticing that all the red spots were everywhere except inside his underpants, which suggested to her the spots were insect bites, and that whatever was biting him couldn't get under the snug elastic waistband of his underpants, nor snug leg openings. In my son's case, it was determined that as it was the hot summertime, and he had been playing outdoors, and rolling in the grass, only in his shorts, tiny mite insects were biting him. As soon as this activity was stopped the 'rash' cleared up. Maybe this is a possibilty in your son's case? It could even be microscopic house dust mite, like from maybe playing on the carpeting? Hope this helps!