If you believe it may be allergy related food is usually the culprit. A lot of times its the wheat/grain components in the food. It sounds like this comes and goes though so unless you've been feeding different food that's probably not it.
Sounds a lot like hot spots. They often are an allergic reaction to sumthin (fleas, other bugs, plants, etc.) I've used tea tree oil sprays on my dogs for years. It works really well on hot spots, isolated patches of irritation, rashes, etc. You may also wanna try a medicated (something like tea tree oil) shampoo and see if that helps. Even an antihistamine like Benadril(sp?) may be in order. Check with a vet on the recommended dose for your dog.