What to do about it
Caulk is a patch. A real flashing repair re-integrates the metal under the roof.
When a leak gets traced to flashing, the temptation, and what a lot of handymen will do, is to climb up and smear a tube of roofing caulk over the gap. It looks fixed. The stain dries. Everybody is happy for about a year. Then the Florida sun does to that bead of caulk exactly what it did to the original seal: it dries it, cracks it, and pulls it away from the surface. The leak comes back, usually worse, because now the water has been getting in behind the patch the whole time and quietly rotting the wood deck underneath.
A real flashing repair is not a surface smear. The shingles or tiles around the failed flashing get lifted, the old or wrong flashing comes out, and new metal goes back in the right order, tucked under the courses above it and over the courses below, so gravity does the sealing and the water is physically forced to stay on top of the roof. For a pipe boot, the cracked rubber collar is replaced, and we often upgrade it to a longer-life boot built to survive Florida UV. For a chimney, the base and counter flashing get reset into the masonry, not just tarred over. Done right, the joint is waterproof because of how the pieces overlap, not because of a bead of sealant praying to hold.
The first step is a free inspection. We send a roofer up with a drone, find every failing flashing point, and put it in a written photo report so you can see the cracked boot or the open chimney joint with your own eyes. From there it is usually a same-day or next-day repair through our roof repair service. If you want the whole roof checked, not just the leak, our free roof inspection covers every flashing, valley, and penetration. One more honest point: when a roof is already getting a full re-roof, the flashing should be replaced new, not reused. Old flashing on a new roof is a leak waiting to happen, which is why a proper roof replacement includes fresh metal at every transition.