Questions about flat roof performance

Hello!
I am in the process of adding a large addition on my home. It is modern in character and has a flat roof. The roof is a two layer system (Firestone SBS Torch on top of Firestone APP 180) installed on tapered insulation, over a plywood deck. It is less than two months old. I live in Maryland, near Washington, DC. As it might relate to my questions, we have hot summers and cold winters here!
The roof is surrounded by a parapet. All the drainage comes to a single opening thru the parapet and is conveyed to a scupper installed on the side of the new house.
After installation, I got up on the roof after a rainstorm and noticed that puddles approximately 5 to 7 feet long and 3 feet wide and 1/2 inch deep are left on the roof. These puddles persist for more than 48 hours, although they get smaller over that time. However, the take home here is that, after 48 hours, there is still standing water on the roof.
In addition to this problem, I noticed a bubble approximately 1 foot long and 2 inches wide in the cap sheet. It is in the middle of the sheet, away from any seams or flashing.
My questions are these:
1. Does this persistence of standing water represent a problem? Is there an generally accepted performance standard for flat roofs that call for complete drainage after a certain time? If so, what is it? The home improvement shows seem to indicate that this kind of roof should be dry after 24 to 48 hours.
2. Does the bubble represent a problem that needs attention immediately?
While I thank everyone in advance for your responses, I'd really like to hear from any professional roofers that might be out there. I'm holding $8200 back at this point, so I think I can get my roofer's attention on fixing these items, if warranted. Thanks again!
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I'd be hard pressed to think of anyone better to call than Firestone.
(800) 428-4511.
Steve.
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Responses inline...

The question is how long does it normally take for water to evaporate. Put out an old cookie tray, its about 1/2" thick, fill it with water, and see if that water evaporates any faster or slower. The fact that its still there after a couple of days might be a good sign - if it was leaking in, it would be gone sooner. "Flat" is a relative term. Is this really flat, or slightly pitched? Seems like theres a "cup" in that area. I'm pretty tough on quality of work but I don't think its avoidable on a truly "flat" flat roof. On a pitched roof, well, it depends on the pitch. I have a "flat" roof with a 1/12 pitch over a couple of rooms. I get puddles, but they're much smaller. A puddle your size on a 1/12 pitch roof would concern me.
The most important thing is that its tight. Remember, you'll have snow on top pretty soon, and heat from the house will melt the bottom of the snow, so you could have standing water there for quite a while.

Might be nothing, but I'd look into that.

If its cold and you're roof is in the shade and its cloudy all week it could take a while to dry off.

You wont' have a problem until it breaks. That could be a very long time, or a tree limb can drop on it and poke a hole. Get a second opinion if necessary.

I'm not a professional roofer, but have lived and worked under mildly pitched flat roofs almost my whole life. So there's my 2 cents worth even if thats all its worth.
S

Make the call.
S
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Thanks for the responses. Here is a little more information:
I have downloaded the technical specifications from the Firestone website for my roof product. In that spec, they say that the roof should be free from standing water within 24 to 48 hours. My roof clearly does not meet this specification. After 48 hours, the puddles are still 2 to 3 feet wide and 3-4 feet long and 1/2 to 1/4 inch deep.
Regarding slope, as we all know, most flat roofs really aren't suppose to be flat and mine is no exception. I don't know the exact pitch, but I'd say 1 to 12 is about right. It was installed over tapered insulation specifically chosen to provide the necessary fall to the drainage hole in the parapet. A drainage plan, showing a schematic of the flow paths on the roof to the outlet, was included in my overall project plan by my architect. So, it was definitely meant to have positive drainage.
S, your point about snow melt on the roof goes right to the heart about my concerns here. I'm afraid that I will have constantly freezing and thawing puddles up there all winter long, working against that roof membrane. It may not fail right away, but I feel sure that this condition will cause a premature faliure on a roof that, from Firestone's website, should have a materials warranty of 10 to 20 years, depending upon how it's installed.
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