[willy]

Tom a couple of pics would help, but from what you describe it sounds to me like the wood that makes up that area of your cuddy top is wet from poor maintenance. The seepage you are getting and the color you are seeing is wood tea I call it. You need to stop it, should have been done when the previous owner saw the first sign of seepage. The water is coming in as you say from where the screws go thru the deck. Those screws should have been pulled, the strip taken off and new sealant such as 4200 should have been put in and then re-assembled.
Depending on how much of an area has been saturated there are ways to repair it. If a small area you will be able to drill small holes from inside and let it dry, shoot a type of epoxy into it while fixing it into correct position with braces and letting the epoxy set up.
If it is a larger area that is saturated you will have to do more extensive core replacement which is something I have no experience in but otheres here have and will give you advise I am sure.
But you do need to seal those holes.