As with all rooftop objects it is important that proper water flow and installation are considered. Flashing that is not layered correctly and sealant applied in the right junction areas allow water seepage. The boot flange was not installed correctly with the proper overlap procedure. Sealant has done a good job covering up the installation error, but is now showing signs of deterioration. Adding sealant may prevent seepage temporarily but is not a roof cycle solution. The boot should be replaced and installed correctly.