3 years ago I had 1/3 of the roof redone and the chimney reflashed. The roofer did not install chimney caps so I had a mason install one afterwards.
2 years ago I had the same roofer replace another 1/3 of the roof, no reflashing done.
The last third of the roof is not near the chimney, appears structurally sound, and only has algae.
So it does not seem to me that water should be coming down the chimney during heavy rains.
Has anyone experienced this? Could the flashing go bad that quickly? Or if rain comes in at an angle could it get in despite the chimney cap?
ETA: I had this problem all the time before the cap was installed. Second edit to correct years.