Thanks everyone. That seems to be the issue. I went out side and stuck my fingers through scupper and felt the old flaps stuck inside. I was able to pull one out and the other one broke off. I will look to replace them. I just can't figure out how the water is getting into the bilge or if it is related to this issue. I can only assume, but it doesn't make sense.
Should the drains be below the waterline? If so, they are well below the water line.
