There are many roof penetrations in a complex building, for roof-mounted air-conditioning equipment and exhaust fans. These devices are usually installed on curbs which are sealed into the roofing material. With time the pitch hardens, and the seals deteriorate. The seals may be watertight but not be completely airtight.
Roof-mounted air handlers sometimes have short duct runs across the roof. The joints and other connections of this exposed ductwork should be inspected regularly and repaired when leakage occurs. Leaks not only upset the air balance of the unit but allow water to enter the ductwork, where it can damage the insulation and cause air quality problems from microbe growth in the damp environment.
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Excerpt from Energy Conservation Projects.