Before you get too far into caulking around the bunk, you might look in the Roo specific section and the General Expandable Discussion
of the forum and read over the experiences of others with the same problem. (There's a couple of them in there) We know that there's a field replacement kit out there to beef up the seals, it has fixed the problem for some, but not all. Apparently Rockwood/F.R. is sending these out to those that call in with the problem and not charging anything for it, which is nice. I have a leak in my front bunk also, at the bottom, right in the middle, but I'm not sure if it's from the hinge or if somehow water is going around the seal down to that area.
Someone had posted a link to their photos of step by step replacement of the rubber seal at the bottom and the rubber gaskets that go around the door, but for the life of me, I can't find it. I'll keep searching and try to get that link to you.
Found it - http://picasaweb.google.com/NickYannucci/RooFrontBunk#
The thread linking this site is Forest River HTT Bunkend Field Fix Kit
Hope that helps.
Where we've been:
2000 Rockwood Roo M-18 Hybrid
2006 Dodge Ram 2500 Auto 5.9 Diesel
Gone but not forgotten -1986 Rockwood 1003 PUP