Roof leak where chimney meets roof
Honestly I can't see this being the chimney.   I know it looks nice and tight but this is exactly why I wouldn't suggest putting the chimney flashing under the shingles.   You now have a seem that is guarded by caulk and not gravity or a harder material like the nice copper flashing.  

So my guess is that the rain came down roof, hit chimney and then entered a hole in the caulking.   Gravity tells it to go to that hole.  Now if flashing is on the outside/over the shingles then the rain has go under the flashing and then over - which is against the laws of nature.   In this scenario a small hole in caulking can go unnoticed for years.