There are several reason why roof windows leak.
1) The window has not been opened for a while and on forcing it open a flashing bends or a pivot hinge works loose meaning the window will not close properly
2) You have had your roof arial repaired or roof cleaned (broken slates or tiles ) resulting in water leaking to your under felt and thus your roof window box
3) You have had your misty double glazing unit changed and they have fitted a non specified unit with out the proper seals
4) The most common problem is loose counter flashing screws resulting in the window rotting on the bottom left hand corner
5) The flashing gullys around your window have never been cleaned
6) Somebody has used your window to access your roof and stood on the main top hood flashing
7) Your top opening bar has never been used as intended for ventlation and condensation has discoloured the pine finish and started to rot the window.
At twice the price of a normal home window it is well worth looking after your roof windows as they take twice the punishment from the elements . Below are pictures of a service and paint