your '09 Roo should have the redesigned seal/hinge system.
unless it was a late '08 that they re-badged as a '09.
the '09-'10 Roo/Shamrock hybrids should have the new seal/frame/sill/hinge setup.
are you sure that you didn't get any of the canvas caught between the seals when you closed it up?
this is a very common mistake with new hybrid owners. especially the more vertically-challenged ones.
if even a small piece of the canvas gets between the frame seal and the bunk door seal, it creates a gap that water can get in.
and leaving a vent or window open while driving can create a vacuum inside, which can help rain penetrate the seals while driving.
the dealer should be able to fix it, if there is a problem with the door/seals.
be sure to check the Expandable/Roo section of FRF.