I too had a roof leak recently with a not so old roof. Finally after I made inspections and couldn't find the culprit I hired a professional roofer and within 15 minutes had it fixed. I must have walked buy the problem as it was a nail that had pulled out and left the tiniest of holes. From the looks of my ceiling stain one would think I had missing shingles. So I felt like sharing an article that will help all of us as everyone will one day have a leak!
Finding that pesky, annoying roof leak can be a real pain and is best left to professionals. That said, most roof leaks happen at flashings. Flashings connect a roof to something that is not a roof such as chimneys, valleys, where a roof bumps into a wall, skylights, plumbing stacks, etc. Check the flashings before spending any time looking at the shingles. (Video by Danny Lipford of DYI) http://ping.fm/NASr7 Danny Lipford says, "Roof leaks can be hard to find, since they often run down the underside of sheathing or rafters to show up far from their actual source. The best time to try and find a leak is when it's raining outside, or you can also mimic rain conditions by spraying water on the roof. Go in the attic and look for damp spots or water stains, trace them back to their highest point, then examine that part of the roof for any potential problems.
Roof leaks can be hard to find, since they often run down the underside of sheathing or rafters to show up far from their actual source. The best time to try and find a leak is when it’s raining outside, or you can also mimic rain conditions by spraying water on the roof.
Go in the attic and look for damp spots or water stains, trace them back to their highest point, then examine that part of the roof for any potential problems.