The warmer moist air in your skylight wells is meeting the cooler air in your room creating the condensation. In cooler months do you notice condensation on the inside of the glass of your skylight?

No, we've never noticed moisture on the glass. The skylights are operable, so we open them to vent the warmer air and that seems to help. But the condensation is not inside the skylight well, but on the flat ceiling surface adjacent to the opening. And it's usually only one side of one skylight -- there's a second skylight only a few feet away, which doesn't have this issue. That's why I wondered about insulation above the area.

Is your HVAC ductwork in the attic?

Nope. We have a basement and all ductwork is down there.