Sooo... Apparently even the roof rack holes in the NBS aren't blind. Or maybe it's leaking where the nutsert meets the sheet metal?
What do you have now, removed rack and put screws back in with some butyl under them or something else?
I just put a layer of RTV under the heads of mine then screwed them back in. We don't get many freezes here and it's only been a few months, though. For my final stage of that project, I plan to use hex socket head set screws with thread sealant, screw them down so they're recessed about an 1/8" then cover them with windshield adhesive. For good measure, I'll smear a layer of the windshield adhesive around the edge of the flange of the nutsert where it meets the sheet metal. Then I'll cover the whole line of mounting holes on each side with low-profile body-colored molding. That'd be like four waterproof barriers, which is 2-3 times the factory amount.