The gas furnance is in the attic (Texas), and the leak was around the vent pipe itself, at the thin gap between pipe and top of conical metal flashing. From inside, there was a thin ring of daylight visible at this small gap around the vent pipe where it goes through the flashing dome. There is a loose rain deflector ring outside on the pipe above, sitting on the flashing dome, but the rain was running down the pipe inside anyway.
The gas hot water heater vent is built similarly, also with a minor leak, but the larger furnace vent was leaking much more.
I dont know if the roofing job needed to mess with the top of the flashing cone (where it was leaking), but I called the roofer back out, and he said they should have sealed it. He put a black sealer goop on it. I think he called the sealer something like MP3 (not all sure I remember right).
Is this how it's done? I assume the furnace vent gets warm, although probably the outside air cools it. Will such sealer last several years? Anyone know of a web site with illustrations how such flashing and vents are sealed?