I have had a similar, but possibly related problem. With the boat stored outside at this time of year I used to get dark patches appearing in the side deck under the areas that one tends to sit. I discovered that this was caused by moisture penetration through the ply from the underside. The varnish/epoxy on the undeside of the deck was very thin and had become cracked due to degradation and possibly due to flexing in the decks. I did consider a thin glass fibre/ epoxy layer underneath, but opted to strip the degraded surface and re-coat with six coats of SP ultravar 2 pack polyurethane varnish, which seems to be successful so far. Only problem was having to turn the boat upside down to undertake thhe task.