2 things:
The dog may be allergic to flea bites, so even if there is only one, that you probably never see, he itches
When my dogs itch, the first thing I look at is their food. Some of the cheaper foods have corn as their main ingredient. That's why they're cheap- dogs do NOT need corn. When I buy the more expensive food, it's actually cheaper. They eat less because they are using everything they eat, and they don't need to see a vet. Though it's certainly not the only higher quality food (everything sold at the grocery store is the cheap stuff) Nupro Ultra is what my dogs eat
I had one girl that was allergic to the Alpo-like stuff the heartworm chewables were made of. Took us a while to figure that out