The most common source of all roof leaks are unsealed or corroded flashings, joints between two roofs, or penetrations through the roof. Flat-top roofs add the problem of backed-up or standing water. If something stops the flow of water off the roof, the water can back up and even rise up over the flashing. Snow and ice cause a lot of backing up on flat-top roofs and should be controlled. If it is leaking when it is warm, and you have tackled all the obvious cracks, check the flatness and slope of the roof. Over the years, roofs tend to move with the rest of the house. Often a section on the roof surface will sag and will no longer have the elevation or slope for water to drain off. If water collects and sits in any spot, it will eventually weaken the membrane at that point. Check the roof on a rainy day and see if there are any puddles. These points will have to be raised from underneath to allow the water to run off. Eventually you will have to redo the roof.