Originally Posted by Darylh
Do you have a attic you can get into, if so the next time you have a good rain go up there and inspect around the skylights for new water coming in. My best guess is the skylights themselves are alright but the flashing and caulking needs attention especially if you have not seen any interior water coming in but a visual inspection in the attic will tell the story.
DarylH is absolutely right about this. The way to locate the leak is in the attic with some good flashlights. You will have to crawl around up there, but you will find the water stains from the leak (i.e. - the roof sheathing, etc). Follow these, they are like a 'trail'. They will lead you to the actual source
of the leak.
As DarylH mentioned, the first place to check if you have a leak like that, is the flashing and roofing areas around the skylights.
Skylight units themselves usually take years to fail (UV light contributes), and it is most commonly their gaskets that get dried out, crackend/peel...and then start to seperate from the glass. Check these after you have inspected the flashing.