not condoning self diagnosis, but I've had a similar problem with my shepherd. I suspected allergies. (not related to food) he had ringworm in the past, which cleared after a month of treatment. then he started rubbing his face with his paw alot. no hair loss...just seemed annoyed. I suspected ear mites...and he was really rubbing his ear/head........treated for that, and he seemed to rub his eyes again. I give him benedryl now because I am convinced it is an allergy of seasonal origin..like people. but...I also started bathing him in Malaseb shampoo. it is antifungal. also am giving him Omega 3 fish oil capsules. the end result...no more rubbing, beautiful coat. in my case I suspected it could be ringworm again (hence the shampoo). in my area there are no vets specializing in dermatology....and I have no faith in my reg. vet. (I can just see alot of guessing and raping of my wallet) my reason for posting is, IF you do not think it is yeast but rather a fungus problem...try the shampoo. use extreme caution not to get it near the eyes. I don't know if this helps at all......just sharing my experience.
hope your pup feels better soon!