i hope you have sorted this out by now but i used to install what sounds like a similar system. i had to position glass in the frame and then run a bead of clear silicon along bottom of unit and 50mm up sides of unit ,then bead (pain in backside)
this was even though frames had drainage holes
(manufacturing design)
levi lewy, July 2008
it sounds like a drainage problem,take units out and make sure the windows are drained or make sure packers arnt blocking the drainage holes
shaun www.sdwupvcrepair.co.uk, February 2008
edit
I can answer this question...
how can i stop water coming through beads on window?