Not sure if this is similar, but my Velux leaks seem to originate between glass and metal at the lower (downslope) edge where water collects, discoloring that part of the wood with occasional drips into the house. Since the flashing and pitch (5/12) is adequate, I figured it was a Velux problem.
So onto the roof I went. After I meticulously cleaned the small amount of moss and needle debris from these areas and drying, I applied a thin continuous bead of clear silicone where glass meets metal and at the lower miter corners which had small separation gaps, and smoothed it out making sure all seams where covered. It’s rained a few days since and so far so good... no sign of moisture.
And yes, I’ll probably have to check (and possibly redo) this fix as often as I clean the skylights – twice a year. Outside of disassembling the unit and resealing the glazing I don’t know what else to do.
CedarRoofsRAPain, October 2009