I've represented Dura-vent and Selkirk in the past. Is the 8 oil or gas, btw? I had systems where the all fuel chimney was stainless and the factory provided AL flashings. Someone used a galvanized flashing and the flue gas "residue" over time got down onto the flashing and rusted it out, which in turn stained the roof. Is your flashing AL or galv? Inadequate chimney height on the leeward side can cause occasional downdrafts which can help "push" flue gas byproducts onto the roof.
my customer called ,she had a new roof put on and now has stains from the metal vent chimney. the house is thirty years old has a newer smith 8 boiler, running well can any thing be done to stop this problem.
Metal outside oxidizes. With steel it's rust. With the metal on the chimney it's probably a darkish powder. When it rains this washes off onto the roof. Those beautiful new shingles help it to show up. It was probably doing it with the old roof, but no one noticed due to the roofs dark color.
Don't take this as gospel.