I had an anchor locker problem, too, but fortunately it wasn't severe.
My problem was that the plastic hose connecting the through-hull and the drain in the bottom of the locker got brittle and cracked over time. So water getting in the (admittedly not well cleaned) anchor locker made nasty stains on the inside of the hull in the hanging locker. After replacing the hose, I dumped gallons of water in the anchor locker, and everything stayed dry inside.
