Right now it sounds like dry skin.
He may also have come in contact with something that dried out the skin on his ears. Maybe if the groomer used a new shampoo or new ear cleaning solution.
If the ears have an odor, then he may have a yeast infection in his ears.
If the flakes turn into scabs, then he could have vasculitis which is inflammation of the blood vessels in the ear. If that happens, he can see the vet and take strong anti-inflammatories to resolve it.
So right now you can treat it for dry skin or a mild contact dermatitis.
You can give him benadryl every 12 hours. His dose is his body weight in mg of benadryl. So, if he weighs 5 pounds, give him 5 mg of benadryl every 12 hours.
You can also apply hydrocortisone ointment to the dry areas three times a day. This should help with any inflammation and itching as well. You can purchase this at the drug store.
He may also be missing important nutrients in his homemade diet. You will want to add a daily multi vitamin supplement to his diet. You can buy these at the pet store, from your vet, or online. A frequently used one is " pet tabs."
www.amazon.com/Pet-Tabs-Supplement-Dogs-60-Tablets/dp/B00028ZLSG/ref=sr_1_6?ie=UTF8&qid=1307389058&sr=8-6 you can order them at amazon.com
I hope this helps