my roof leak

Well i finally went up to my roof with a flashlight and looked down the two oldish opened flues.
One seems to go all the way down, and I don't know if its mine or the neighbors, but it looked to be in reasonably good shape (built in 1896 good shape that is).
The second flue is sealed off at roof level. That is to say, when you look down it you see dirt at about roof level. This is where I saw water on the night it began to rain. So I'm hopeful this is the source of the leak and I'm planning to seal it up.
Should I seal it up airtight or put a cap on it? Is there any thing that can go wrong by sealing it up? Moisture, mold, etc.
-Ben
PS: I also looked down my radiator flue. The masonry looks allright, but believe it or not, about one story down there's a metal suitcase in the flue! It's like an aqua blue metallic briefcase/suitcase thing - looks kinda like a lunchbox but bigger. Who the hell knows why its there, but there's plenty of space for air flow.
I'm thinking it's either:
1) there to brace some failing masonry
2) full of money from a previous, criminal, owner
3) full of some dead person, killed by said previous owner
:)
i don't know how the f*** I'm gonna get it out of there.. magnet on a fishingpole maybe?
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Radiator flue? you mean heating system, likely a lunchbox of a worker fell in, remove it. Use a cap to keep out water
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