Puff-backs can happen when a boiler is fired up with a chamber entirely full of fresh coal...hence AA's recommendation of filling the combustion tube about half full with ashes prior to adding coal. I realize a lot of people don't have ashes on hand when a new boiler is installed, but if you do...it is wise to follow the directions.
Matt, was that stovepipe the ultra-light gauge stuff? Might be worth using some quality black stovepipe and non-adjustable elbows if you can get away with it.