My bees did the same thing. I think the answer is to make a top cover that has the "flaps" on the sides rather than on the front and back. I haven't tried it myself, but have seen other set-ups like that.
Bees fill all cracks based on the amount of light they let in. The top lets in a lot of light and gets stopped. The bottom board doesn't let much light in and it doesn't get much propolis. They seldom propolize a screened bottom board and it's letting a lot of air in, but it's not letting a lot of light in.
If you make a way to let the air out and not let the light in, they won't propolize it so much. But where would you get your propolis?
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