I have seen other people adress this same problem, but have never heard a solution. I make and deliver bagels here in my home-town and my business is steadily growing. I use the bagel recipe from the King Arthur website.
They taste great, but they are always, always bumpy. When they are boiled they shrivel up as usual, but when they bake they puff out and look great straight out of the oven, but as they cool down they become bumpy again. :(