Steve, no unfortunately I don't have any advice for you. I am myself still looking into setting up my roof for gardening, and am still undecided how to precisely do it.

We have similar concerns here: our roof is fairly new as well, and of course, we do not want to damage it.

Do you have your containers directly on the roof or do you have a deck installed?

The fluid under the membrane would worry me. If the roof was done by a pro company they often give warranties on roofs (10 years or so). However, extensive walking on the roof would probably void that warranty. Any way, I would look into that first.

I am sure some experienced handy people will have some insight, but my guess is that the membrane got punctured somehow and that's how the fluid got trapped. It shouldn't be too hard to fix that, but my main concern would be how to avoid it in the future.

Anyway, I have not been very helpful, but I am very interested and would like to learn more about your set-up.

Oh..water under the membraine came in from somewhere above where you find it.. best to remove the break in the syatem and then work on the water you have.. you can go into it on the downslope side and lance it like a boil.. drain the fluids and seal.. then see if the leak you found and fixed at first was the cause..
Otti.. well I've been on the roof for a decade or so.. just walking and gardening on the rubber membraine.. with only sparotic breaches in it.. care has to be given to chair legg section.. and thoes of tables and any other garden item.. so it doesn't come to a small section and puncture the roof.. like my chairs have a support from the front leg to the back to disperse the weight.. and theffront and back legs taper nad round over the the other os tipping won't puncture the roof.. I also grow a lawn right on the rubber.. this is a good way to minimise the effect of walking .. ot have a buffer of lawn under foot..[ The new plands for the remake of Lincon Center here have the resturant with the grass roof .. although a decorative only one due to it's shape and form]
if you are looking for a covering for a roof.. there is this product.. although I have no first handknowledge of it's functionality their claims are lovely.. and it's just applied over the deck you have
www.globaldecking.com
best of luck in developing the roof... Gordon

I have no experience with rooftop gardening, but I find it fascinating and a most important activity to develop. I found an article on the subject of container rooftop gardening. It is an experiment taking place in Montréal.

http://www.alternatives.ca/article1165.html

This document about the same projet is in french but contains many pictures. Isn't a picture worth a lot of words? :)
http://www.alternatives.ca/IMG/doc/Jardins_hydro.doc

Here is a link that might be useful: Urban Agriculture Reaches New Heights Through Rooftop Gardening