It sounds like it could be allergies. Callie has allergies and takes Hydroxyzine and a new symptom she developed this year was itchy ears. When she was rubbing them I took her to the vet and she looked in her ears and put the qtip in there to get a sample to look and see if there was an infection she could not see and there was not so she said make sure I am giving her the allergy medicine which I had not been doing everyday because the weather had gotten cooler and sure enough no more itchy ears. If they do start itching I give her the allergy medicine and then after a little bit they dont itch any more. If a vet has checked her ears and there is no infection then I would think it is allergies. I hope this post made sense I am so darn tired