Scratching but no fleas

[TheRealAmyFarrahFowler]

My 3yo scratches a lot. Mostly around his ears, cheeks, chin and neck. I have gone through his fur with a fine flea comb loads of times - most nights. He likes it so I can be really thorough. I have found nothing - no fleas and no evidence of fleas. Last time he had fleas there was obvious flea dirt in his coat and the comb found the fleas.
What else could be making him itch?
His skin isn't red or angry or enflamed. No lumps or bumps. Otherwise very healthy and happy.
Any ideas?

When was he last at the vet - and when was he last treated for fleas and mites? (I'm wondering if he could have ear mites.)

He's due at the vet in the next month for his annual boosters. I did think ear mites but I clean his ears out quite often (they're huge and he loves having them cleaned out ). There doesn't seem to be anything there that there shouldn't be but I don't know how possible it is to see ear mites. It seems to be more his cheeks and neck - you know that scratching where they seem to punch themselves at super speed with a back foot. I'll definitely mention it to vet.
I treated him for fleas about 3 months ago. I used an expensive spot on the neck brand and combed out a few dead fleas a few days later. Completed the course (3 treatments) and had no evidence of their return since.

My cat suffers from food allergies, I recently tried her on Encore a new brand of cat food, unfortunately this has made her flair up with a itchy lower back, bum area and around the jaw. Steroids are often the answer, could also be stress. It was defintely that with the arrival of Lil Smeared.

I would take him to the vet sooner rather than later. You need to know what's going on.