Milipoo, two of our dogs start scratching all over after a dose of topical flea/heartworm treatments. It only starts about 4-6 hours after it's been applied and can last up to 48 hours. There are two brands we can no longer use but have found another that they haven't reacted to so far. If your pup is still itching, perhaps you can bathe her using a very mild (no perfume) shampoo made specifically for dogs.
Your vet will prescribe something for your pup's ear infection and, at the same time, you can discuss other forms of parasitic control.
"Education is a progressive discovery of our own ignorance." -Will Durant