Telling you why a roof leaks is akin to telling you why it rained in the first place. You should make certain the roofer specializes in flat roofing and preferablly in the type on your building because they have little in common with metal or 3 tabs. Is it modified bitumen ,EPDM ,torch down or other?

Also what type of skylight, curb, flashing was used? How did he determine where it was leaking? Leaks have been known to show quite a ways from where the actual leak is. klem is probably on to something also as the roof was repaired and the old skylight removed and a new one installed so that is a lot of work in section of roofing.

@klem1 - I believe it was torched.

@millworkman - we had to make the roofer did several different tests (at some point we thought it was the screw holes on the flat skylight that was leaking - so they caulked it and still leaked). We finally had to wrap a tarp around the skylight only, and that seemed to stop the leaking. After the new, doomed skylight was installed, the only leak that occurred appear to be the same as before - at least from where I can view inside, it was coming through the same area / holes as the leak before.

I am not a roofer but have hired many roofs repaired and replaced. This I can tell you. After replacing a skylight on a torch down roof there shouldn't be a screw head on top of membrane. Any visiable screw should be in the shadow of skylight flashing and at least 3" above horizonal surface of roof. "IF"you are able to stop a skylight leak with caulk,it will soon return due to expansion and contraction of all the different material involved. The more i hear,the more it sounds like you need a different roofer. As if you don't have enough trouble,I have somthing that will distress you even more. Leaks so small they seldom or never drip indoors can and will rot the structure out. Out of sight,out of mind roof leaks are to building what cancer is to humans. Use good roofers,they are cheaper over the long haul.

Was the skylight installed with screws thru the flashing? It sounds that way. That was why I asked what type of skylight it is.

The old skylight has screws through the flashing. I looked around briefly at the new skylight (after it was installed) and didn't see any screws, so I assume that's no longer the case now (I hope!)

You still have not told what type of skylite and how it is flashed? Directly an the roof or on a curb? Continuous flashed or step? If a curb mounted how tall is he curb? We need to know if this is truly a skylite designed for a flat roof.

"We need to know if this is truly a skylite designed for a flat roof."

Agreed. In fact I believe pictures are required since op doesn't speak nor recconize industry standards for install. And if there is no curb,there will probily be leaks from time to time.

Sorry, I'm not very familiar with the technical/correct terms, so I'll do my best trying to describe what we have:

- the new skylight is domed, and appears to "sit" on a raised frame above the roof, and the skylight covers the entire frame, and "goes over" the frame as well. I don't see any nails on the surface / edges of the skylight

- our old skylight was flat (on top of a flat roof), and the roofer told me that was not right. Should have been a domed one so water wouldn't pool/sit on it (hence, the new skylight is domed).

- I'll try to get some pictures in the next day or two.

Thanks much!

Domed skylites are acrylic (plastic) and in my opinion worse than flat (which would be glass) Water pooling would not be an issue with the correct skylite in the correct application but skylites for a flat roof are handled and manufactured differently than for a pitched roof.