My son dealt with this last year, and, despite what your pedi told you, it is MOST CERTAINLY contagious (it's even in the name). Basically, the bumps are filled with a virus, and, if you scratch them, the virus (and bumps) spread to the surrounding skin plus anything else you happen to touch right away. They do go away on their own, but it can take 12-18 months -- especially if you keep getting new ones. The dermatology department at Texas Children's offers two different treatments -- freezing them off (which I was told is worse than having them in the first place), or this serum that is made from the venom of a South American beetle (I realize that it sounds crazy, but it's true). The "Beetle Juice" (as we call it around our house) is applied in the office, and then you wash it off a couple of hours later. After a couple of days, the bumps scab up and fall off. It doesn't work for all people (it didn't really work for us), but, as I said, those are the only treatments that are approved by TX Children's. Your best bet is to see a pediatric dermatologist (be warned, many, including those at the hospital, can take 6 months to get in to see), and have them confirm the diagnosis, and help you choose the best treatment. Unfortunately, according to a friend who is an adult dermatologist, pediatricians don't often know a lot about it. But, please, what ever you do, DO NOT scratch them or do anything that will break them open!!!!
Good luck!