Hi,

Have a gander at how the skylight sits on the gasket, from the outside. As the plexi swings down into the gasket it should be more or less horizontal when it contacts the gasket. It could be that the plexi is contacting the gasket at the forward edge too soon. Know what I mean? It might be that the hinge straps are bent. 

Or it could be that the hinges are not positioned quite right and the skylight is not aligned with the gasket in plan view.

I agree that it seems hard to believe that water gets in seeing as the gasket is raised above the roof. But it can, maybe it's capillary action.

And as others have mentioned, be sure the fasteners to the roof are well sealed with mastic,
Dum-dum. I like that stuff much more than caulk.

Alistair 

> On Sep 24, 2016, at 9:18 AM, Loren Busch <starwagen@GMAIL.COM> wrote:
> 
> ​ RE: Skylight Leak
> The only leaks in the skylight that I have ever had to deal with have been
> through the screws that hold the skylight to the hinge.  And careful
> tightening of the offending screw stopped it.  Don't tighten to much you
> can crack the skylight.