It could be allergies. Environmental are much more common than food, but because it's the ears, I'd think food too.
I'd do the Rx diet for at least 12 weeks (with no other food or treats given) and see how she does with that and the Synotic. After the Synotic if it still hasn't cleared up (as you're finishing the food trial) you can try another ear med for yeast (Zymox or Otomax). Some of these drugs work better than others and some just depend on the dog. I've used Mometamax and didn't like it much.
If the vet is very convinced that it's food allergies and the in-the-ear drugs aren't making her comfortable, he could potentially give a steroid injection to give some relief. Synotic should do a pretty good job of that though.
If after 12+ weeks there is no improvements with the food change and drugs, then you'd be talking about other causes (enviro. allergies, something else that needs to be treated in the ER, systemic yeast issues, etc.).
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