Allergies do make dogs itch and it could be inhalant allergies or food allergies causing this or even contact allergies.
If you are feeding a grocery store food you can see if swapping to a food with alternative ingredients will help. Wellness, Eagle, and Dick van Patten are foods that make formulas based on fish, rabbit, duck, and venison and have no grains or alternative grain like oatmeal and that might help your dog.
You can also see if Benadryl at a dose of 1mg per pound of dog helps with the itching. You can give a 12 pound dog 1/2 of a plain (not cold capsule) 25mg Benadryl tablet every 8-12 hours. Its not a cure but might help the dog feel better.
Also itching can trigger skin infections with bacterial or yeast which are itchier than the flea bites for some dogs. You may need antibiotics or a disinfecting shampoo like a chlorhexaderm shampoo to clear this up.
If your vet cannot help you ask for a referral to a veterinary dermatologist or see if you can find one here
http://www.acvd.org/site/view/55607_FindADermatologistAlphabetical.pml
Hope this helps you!
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