Much of the chimney flashing and repair work being done is far from acceptable industry standards. There are many reasons why a chimney will be repaired incorrectly, but there are very few reasons why a chimney should be repaired incorrectly. Often a homeowner cannot afford to hire a roofer and will do the repair themselves. Without the proper tools and equipment, a chimney flashing repair can be a daunting task and the repair will inevitably fail.
Sometimes a handyman or inexperienced roofer will be hired to do the work and fail miserably at the task.
Many times a fairly experienced roofing contractor will be hired to do the job, but as the chimney and surrounding area are usually inaccessible and unseen by the homeowner, the roofer will choose to do a quick, lousy job to make extra profit.

Here are some flashing installations and repairs I have seen that were just wrong.

Stone Chimney without Counter Flashing

This chimney is on a large slate roof and was repaired with copper flashing. The cricket was installed poorly with simple seam laps that were caulked and face nailed instead of soldered. The roofers left off the rear counter flashing, (they installed the side counter flashing that was visible to the homeowner), and just caulked the sub flashing to the chimney.  This particular job started leaking about a year after it was finished.

 

Cultured Stone Chimney without Counter Flashing

A cultured stone chimney on a new house with asphalt shingles.

Installed when the house was new, this chimney has a one piece aluminum apron, shingle tins and one piece saddle flashing. All are caulked directly to the masonry sub chimney and nailed to the roof decking. There is no counter flashing. The roof decking has settled separately from the chimney breaking the seal on the flashing and causing leakage.
It appears this was a tag team effort by both inept masons and roofers.

Brick Chimney with Thin Aluminum Flashing

This brick chimney was re flashed as part of an overall roof replacement. The flashing material is a thin painted aluminum sold in a roll and usually used by siding contractors. It looks like the roofers did not have a metal break to bend the metal. The two piece apron metal was just nailed at the edges to the roof and pushed into the chimney. They might have used a piece of wood to make the top bend. It has since buckled and the caulked seam is now open to the weather.
The joints at the masonry were the caulked with a cheap tar. The original mortar must have begun to fall out and left large gaps at the old flashing joints. The roofing contractor tried to fill the gaps with caulking and it had run out of the joint.

Caulked Copper Flashing on Clay Tile Roof

A typical repair to a leaking chimney flashing. This older copper flashing probably started leaking at a loose saddle joint or possibly a broken tile around the side or rear of the chimney.  It may have also been leaking at the counter flashing/masonry joint. Often the first attempt at repairing the leak is a haphazard caulking of any and all seams, joints, or openings near the chimney. Here the counter flashing has been caulked. There was caulking pushed under the front apron flashing. The gap between the side roof tiles and chimney were filled and the rear saddle has been covered with tar. All this tar makes it virtually impossible for an experienced roofer to find the initial leak to make a proper repair and usually the whole chimney needs to be re flashed.