In most cases, leaks come from a penetration to the roof, maybe a pipe vent, chimney or even a puncture in the roof.
This is the problems with Chimney's. Most people will think "I'll just caulk it" or i've heard the expression "There is no such thing as too much caulk" a million times.
Most of the time there is a simple fix that doesn't require you to over load a tube of caulk all around your chimney.
Here's an example of a chimney that needs to be re-flashed.