Have you checked your pup's ears also?
I suggest you use frontline plus for your puppy instead of using anti tick and flea shampoo. Scratching might also be a sign of an allergic reaction to food, shampoo, etc. Try eliminating the cause one by one. For example, try changing the brand of shampoo you are using. If the scratching doesn't stop, try changing the brand of dog food, and so on and so forth. I know this is a very long process. But try checking his ears first or use frontline plus.
Please update us with your puppy.