Dear Vidya
In my view the treatment done on the roof either have cracks or formed undulation that creats water pool in rainy seasion. There is possibility of that mouth of rainwater pipe may have cracks and leads to leakage. At the website gharexpert.com in the ROOFING & CEILING AND IN DAMPNESS sub section of construction you will find lot of articles for the solution of your problem. for ready referance see the article link given below
http://www.gharexpert.com/articles/Roofing-Ceiling-1998/Roof-Leaks--Causes-Repair_0.aspx