Windows may leak or develop leaks if they're not installed perfectly, i.e. level and plumb. A poor installation will cause the window components, including weather stripping to be mis-aligned and therefore allow water leakage.
You can check this yourself using a 2' level. Hold the level against the side vertical rails of the window and if they're fairly far out of plumb, then that may cause a leak.
If you've had a lot of settling in your home, then that may cause the windows to mis-align and cause leaks just like a poor installation would.
Another cause of window leaks would be a lack of proper flashing above the windows. There should be sort of a "Z" shaped metal flashing out the outside of your home that tucks up behind the siding, bends across the top of the window itself, or above the horizontal trim board above the window. The flashing should then bend down the trim board by about 1/4". Properly installed flashing can prevent many window leaks.
Another possible fix would be to make sure the windows and adjacent siding/trim boards are all fully caulked. Exterior caulking is one of the most neglected items in home maintenance and it should be checked and repaired every couple of years or so.
You didn't say where the windows were leaking from (i.e. from the top, the sill area etc.). Without looking at it, I would suggest that you check to make sure the windows are installed level and plumb first. Then check the flashing and caulking.
These items will repair almost all window leaks. It's actually pretty rare that a roofing problem will cause a window leak without causing other damage such as stained drywall on the ceiling near the leak area.
Source: J. G. Hamm Construction - Ypsilanti, Michigan