Answering the “politics” of this question is not really the focus of this post however.
Nor am I going to go into issues related to water leaks due to poor flashings details. The reality of skylights is that newer units with proper flashing kits designed specifically for that particular skylight are VERY good at keeping water out. Most leaking associated with these skylights is due to installation errors—not due to anything inherently wrong with skylights themselves.
Today I want to discuss improper installation of the skylight well (those structures that make up the transition from the interior ceiling to the skylight itself.
In this picture one can see this transition structure in the attic wrapped with yellow fiberglass insulation.
Notice the little grey stain on the sheathing at the top right corner next to the truss. This grey stain is where warm moist air is moving from the bathroom interior space into the attic. Moisture condenses on the sheathing turning the sheathing grey. Under the right conditions this “grey” might actually be mold as well. In this next picture, another skylight in the Master Bathroom of the same house—–the bathroom that gets used the most—–shows even more pronounced staining than the first picture. Note that there is staining of the roof sheathing at both corners. Over time this moisture can weaken and damage the sheathing. In the winter it would not be unusual to see the grey areas covered with frost in cold climates.
This condition is the result of poor air sealing of the connection between the skylight and interior wall surfaces and is a relatively easy thing to fix—-preventing heat loss and saving energy.