Chris,One thing you may want to try is some Trim-Lok gasket material around the top of the drain gutter dam like this stuff...What happens when it rains a lot is the gutter fills up faster than it can drain off through the channels molded in the deck, and then it just spills over into the fishbox. Take some pieces of modeling clay and form them into small balls about 1/2" high. Set them on top of the damn, then close the lids. Open them back up, and measure the thickness of the clay. That's the thickness of the material you want to get. Good weather stripping would probably work as well.
Chris, take a look at this pic...There is a raised area adjacent to the gutter drain, we call that the "gutter dam". The gasket goes on top of that dam, and seals to the underside of the lid.