what you might have to do is put the plugs in at the dock, then pull them when you are underway in order to drain that last water out, then obviously put them back in. or you can get the flaps or pingpong style of scupper that are supposed to stop this from happening.
Ball Scupper
http://www.thmarine.com/product.cfm?PRID=55
Flap Scupper
http://www.thmarine.com/product.cfm?PRID=57
this is a comon problem on a lot of boats. my old mako sat so low in the water that the scupper (there was only one) was glassed over. I had a hole going to the bilge and all water was pumped out. you want to talk about sleepless rainy nights....
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