For young puppies the three most common causes of itching are dryness, fleas and mange(microscopic mites in the skin). Since there was a recent flea treatment and if you utilize the test in the video about fleas and don't see any evidence then dryness is the most likely. The protective layer of the skin (epidermis) in dogs is actually thinner that in people so even products like baby shampoo can add to dryness problems. Using a mild puppy shampoo (eg. Aloe and Oatmeal) and avoiding frequent bathing is a better approach. When you visit your vet make sure to mention the itching so they can assess the problem and see if a skin scraping is necessary to rule out mange mites.