...appears to be something pretty basic. Apparently the caulk around a smoke pipe is bad and water was leaking straight in.
So the good news is that we don't need a new rook, or even part of a roof. The bad news is that it appears our shitty builder slapped the thing together with caulk rather than proper flashing, so I assume it's only a matter of time before the other pipes leak. Depending upon the cost, I may go ahead and have the roofer properly flash all of them.
I'm beginning to think that caulk, as used by builders, is the devil.
Oh man, that's really good news considering what you were thinking. How old is your home? I am terrified we will run into similar stuff once we move into the house.