jim laid this down on his screen :
The only difference we can see (without starting to rip it all down)
is the lap of the flashings - the problem area has a 2inch lap between
the bottom flashing of the top window and the top flashing of the
middle window, the other velux has a 6inch lap at this area.

If I understand your explanation correctly, a 2" overlap is nowhere
near enough to prevent blown rain entering on a normal roof slope
angle.

--
Regards,
Harry (M1BYT) (L)
http://www.ukradioamateur.co.uk