This is a common area for core problems. I am not sure of your exact model but in my case I know water was getting onto the core through the hole for the sliding handle/pin handware that locks the lid into the deck. I cut out a section of the lower skin about 1'X2', removed the core, replaced the core, and glassed in a new lower skin. I did not replace the core in the immediate area of the sliding pin, instead I filled that section with thickened epoxy to stop the problem from happening again.
While you are at it, I would remove and rebed the anchor pan and check for rot in the bulkhead below that wet section of core. While you have the anchor pan out you might as well remove, epoxy fill, redrill, and rebed all the bow hardware that you cant do without removing the anchor pan.
Sorry, you are not alone. The pictures show the culprit and the damaged core removed.
http://www.ericsonyachts.org/infoexchange/showthread.php?t=9357