Here is a good example of how water enters your chimney from a rusted chase cover. Here is the first picture showing what it looks like from the top:
Now lets take a look around the center flue termination from the bottom side:
Not looking good! Now a even closer look. Notice the light shining through the small pin holes:
When you see a rusted chase cover on your roof or signs of rust staining the side of the chimney, it may be time to replace your chase cover to prevent water intrusion.