Yeah, my problem with water leaking at a (plumbing, not burner) vent
stack turned out to be the roofers not installing a flange.
Before I realized that, my first thought was to cap the vent (there was
no cap initially). When that did nothing I decided to rip out the
damage in the kitchen ceiling and there it was -- the back side of the
shingle. The rood deck is 1x4's -- nothing like a round pipe going
through a square hole to cause water damage.
My solution was strategic caulking (with asphalt caulking) under the
shingles, around the vent (primarily above, of course). So far so
good, but I suspect I'll have to revisit it.