I have seen a number of chimneys without cap flashing, a somewhat common occurrence in reroofing jobs. In this case, asphalt cement is used to seal the joint between the step flashing and the chimney, but this frequently results in roof leaks because water is able to penetrate at the point where the flashing meets the chimney. If this is the case with your chimney, you can correct it by removing mortar and setting cap flashing into the joints. Then tuck point mortar back into the joint and bend down the cap flashing. This is hard and skilled work, and in most cases it's best done by an experienced mason.
Water can also leak in if the chimney was installed without a cricket.
The cricket prevents debris or snow and ice from piling up behind the chimney, which would cause rain or melting snow to back up under the shingles and leak into the house. The cricket also deflects water around the chimney and then down the roof to the gutters. All rights reserved.