Skylight Install Issue

Last week, I had my house re-roofed, and they seem to have done a good job. As part of the work, they replaced a skylight. In the room where the skylight is, there is a smell of roofing cement. Actually, the smell travels throughout the house because it gets picked up in the air conditioning system, but is strongest near the skylight and especially in the heat of the day.
I went up on the roof to take a look, and noticed that there is roofing cement on the place where the skylight fits onto the sheathing/frame. In other words, they put roofing cement on the plastic itself where it contacts the metal sheathing/frame. The skylight seems to be nailed in properly, and nothing leaks.
I assume that the sun is heating up the roofing cement and the smell is coming downward from the skylight. Which leads me to my two questions:
First, is putting roofing cement where they put it, as I described above, the right thing to do? Though I have no experience here I would think that nailing it in is enough, and that putting roofing cement where they did would make it difficult to remove the plastic if ever necessary. Second, will this smell go away over time?
Thanks,
Ross
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Everything goes away over time but seriously how much roofing cement did they use ? It shouldn't be slathered all over. What does it smell like, tar ?
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scribbled this interesting note:

It is good that nothing leaks...

Without seeing the skylight in question, I'll hazard an answer...in short, NO.

I don't know how your skylight is designed. There are a few different variations. In none of the ones I'm familiar with should you ever have the smell of roof cement come inside the house. Something is non-standard with the installation and if I were you, and was unfamiliar with how to do this kind of work, I'd call in another, better qualified individual who could get an eyeball on it and give you some on-site guidance.
http://www.google.com/search?q=skylight+installation+instructions&hl=en&lr=&start=0&sa=N for a number of different kinds of skylight installation instructions...
-- John Willis (Remove the Primes before e-mailing me)
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It has been a number of years since I did this kind of work but its sounds like a poor fit was 'doped' with a lot of asphalt. The metal flashing is supposed to do the bulk of the work with a little along the top edgewhere it should be up to/ under a flange along the edge of the light. This flnge is supposed to do the deflecting of the water and the asphalt just stops any backwash in a storm.

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Unless the skylight is open, nothing that they put on the outside ought to be affecting the air on the inside. (if it does, you're going to have an interesting heating season....)
So there has to be sealer, or tar, or something, on the INSIDE of the window, unless you're just confusing the smell of new vinyl, with that of cement. If it's the latter, it will stop eventually. Grab a chunk of PVC pipe, and cut it with a fine-toothed saw or file. Is the smell anything like that?
--Goedjn
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Thanks for your responses. I think the smell is roofing cement, rather than new vinyl, and the roofing cement is in fact on the inside of the skylight where it contacts the flange. The roofer came out and looked, and said that they put the roofing cement there as a leak precaution, and that the smell should go away in a day or two. Well, they did it Saturday--two days ago--and it still seems strong to me, especially when the sun is beating down on the roof.
Ross

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