How did you repair the cabintop and deck? We had problems with delamination in our cored cabintop, and so attacked it from the inside, cutting out fiberglass and removing rotted and wet core material. We then let the "opened" area dry out as much as possible over several weeks with fans & heatlamps. From your description, it sounds like you didn't open up enough, and that there's still water (with rotted material turning it dark)spreading rot spores inside the laminates. Water inside the deck laminates may have migrated there over YEARS of use. It may leak out even more slowly, especially if you've repaired the deck and there's now no incoming air to displace it inside the deck. The deck may still be sound, and may stay that way for a good while. It took about 20 years for a screwhole in our bilge to create a delamination in our hull about 2' in diameter, which I fixed a season or so ago. If there's water coming out though, the problem isn't going to go away. Freezing temperatures will make it worse sooner, of course, with the expansion of the ice between laminates. The repaired holes in the deck may also not have been the sole source of water ingress. Any fittings,
hatches, tangs, nicks or dings could also have been (and still be) responsible. It is annoying to have to worry about water getting into a boat not only from the bottom, but from the top as well. Maybe that's what makes
dinghys so popular.