Jim,
Yours I think is the newer layout below, with the head aft on starboard and the galley aft on port. Mine is the older layout with the galley aft on starboard and the head forward of the saloon. Mine has four cockpit drains, two outboard and two inboard; the inboard pair discharge under the stern counter via individual seacocks, after their hoses cross in front of the rudder post. But the outboard pair come together in a tee in front of the rudder post, and then run in a single hose all the way forward to a seacock right under the galley sink. It's this longer run that may have the potential to hold rain water if the seacock is closed. This arrangement has been discussed elsewhere on this site, but I don't recall owners of later models detailing the routing of their outboard scupper hoses in those discussions. If yours passes an area where it's inaccessible on its way to its seacock, that may be a potential leak spot. But if that cockpit drain WAS the source of the leak, you would expect it to stop producing water after its limited reservoir was empty.
Dan Morehouse
1981 E-38 "Next Exit"