I have heard dozens of reports of dogs losing the hair on their necks where flea products have been applied, and most of them have involved Advantix. I don't use it, I use FrontLine Top Spot instead, so I can't speak from first hand experience, but like I said, I have heard of others having the same problem. Next time you have to apply a flea preparation, try one of the other ones and see if you have the same problem. It could be that your puppy is just sensitive to the ingredients, and then again, it could be the Advantix in particular that elicited this reaction. Only time and process of elimination using other flea meds will tell.
Ghilly
"Negative" for what? I assume your vet did the scraping suspecting mange mites and didn't find any. It certainly sounds like your dog is having an allergic reaction to the advantix, and if he were my dog, I would discontinue using the product and see what happens.
An alternative for flea control is the heart worm preventive, Sentinel. I live a hugely flea prone area and Sentinel has worked wonders. It renders any biting flea sterile so you don't get the house and yard infestations. Many people use Sentinel along with products like advantix, but I've never found it necessary. As long you regularly bathe your dog with a quality flea soap, no advantix is needed.
Take a hard look at the label on the dog food you're using. Your dog may have a bit of a food allergy, and grains are the fist culprits to consider. It's also a good idea to give any dog a daily multivitamin to maintain top-notch nutrition. Dr. Cheng on Med Help's "Ask a Vet" forum recommends Missing Link. It's rather pricey in my experience, but again, label reading through the different supplements in the vitamin aisle at the pet store can pay off. Make sure you have your reading glasses if you need them - like me! :-)