it is important to have a good quality skylight, Velux is one of the best, we have four installed on our home two have been on trouble free since 1993. And it is a Must to have the Velux flashing kit that matches the window you purchase and have it installed under the shingles properly.
A good quality skylite/flashing kit, installed properly by an experienced roofer/contractor will last as long if not longer than the roofing shingles and not be a leak problem. Thats why I suggested you get a reputable roofer/contractor to see if yours can be repaired properly or if it mgiht warrant replacing them with a good quality as I mentioned above or even eliminating them if you dont mind losing the natural lighting from them. Hope this helps. LJ