I had a similar problem a few years back with my Westsail 43. We had removed the galley pulled the deck and both center line water tanks and the center line fuel tank. After chipping away and cleaning 40 years of worth of sludge and crud the bilges were bone dry and sparkly clean.
You can imagine how we started freaking out when we started seeing water seeping up from right over the keel. I dove the hull over and over looking for were the water could be coming in from. Had heat lamps in there for almost two weeks trying to stop the slow leak.
I finally called Bud, and he explained about the plywood that was glassed in the bilges over the keel. Drilled and pulled a few plugs out using a whole saw and discovered that the plywood was soaked through and rotted. I was able to grind away all the glass around the plywood, pull it up in one piece, reclean and dry the bilges, and NO MORE LEAKS.
I reglassed a new piece of ply wood down and went back to the original projects.