The cockpit drains into the centerboard housing.  Flushing with lots of
water while the centerboard is down should eventually get ride of any
accumulation of mud trapped in the box shaped housing through which the
drain flows.  Once your remove your centerboard you could get at the
underside of the drain.  It isn't a big opening and it can get partially
blocked.  Inside the cabin, the bilge does not drain.  What you are
finding is probably the accumulation of years of dirt - or the grunge
deposited through a leak at the backside of the cockpit drain housing.
Slapping some fiberglass (or 1,000MPH tape) around the back of that box
should stop the leak. A mirror will help you analyze what is going on
back there.