Without digging too deep did you obtain 'Permitted developement' permision from you building control office at the town hall?.
The problem is the builders problem so get them back to put it right.
It will most likely be due to two or three things. The flashing at the top of the roof has come away from the wall, if so it wasn't put in properly. They used 'Flashband' Which I think is not permitted form of flashing on a habitable room or simply applied mastic between the wall and roof which is illegal as far as building regs go.
If you get no joy from the builders then name and shame them in the local paper but only if you have proof they are the builders that did the work.
Take a digi photo of the roof then a close up of the roof top and I'll look to see what type of flashing it is. robertwhiting76@hotmail.com
Bob
February 2007