Hmm. If your sure he doesn't have fleas, we can rule that out...
The only thing I can say for sure, is if he's been swimming a lot. Roxy and I just went through this, and being in the water so much had dried out her skin.
I used this Oatmeal Anti-Itch stuff, and it works... She hasn't been itching since any of her baths and I imagine she won't need anymore.
Have you changed foods or any part of his diet?
Could it just be normal mosquito bites?