Sauté onion and green pepper in 1/2 cup butter in a heavy skillet until tender. Stir in 1/2 cup flour; cook over medium heat 10 minutes, stirring often. Add crab meat; stir well. Press mixture into bottom of a lightly greased 13- x 9- x 2-inch baking dish. Set aside.
Place water in a large Dutch oven; bring to a boil. Add shrimp, scallops, and flounder; cook 3 minutes. Drain, reserving 1 cup cooking liquid. Set seafood aside.
Melt remaining butter in a heavy saucepan over low heat; add remaining flour, stirring until smooth. Cook 1 minute, stirring constantly. Gradually add milk and reserved cooking liquid; cook over medium heat, stirring constantly, until mixture is thickened and bubbly. Stir in Cheddar cheese, vinegar, Worcestershire sauce, salt, pepper, and hot sauce. Add shrimp, scallops, and flounder; stir lightly.
Spoon seafood mixture over crab meat mixture; sprinkle with Parmesan cheese. Bake at 350° for 30 minutes or until lightly browned. Serve immediately.