My first thought, and I hate to say it, but if you have an inside animal that is in your son’s room often, it could be peeing in there. I read a report on dogs in the house and they DO urinate in the house in small, undetectable amounts even if they’re trained to go outdoors. It’s not really a big deal since you clean/sanitize often, but even clean homes can have lingering scents if they have an animal indoors.
That said, I would love having a cat or dog indoors though, and plan to do that one day after all my kids are much bigger! 🙂
Also, I second keeping play shoes in a separate mud room!