I don't think I did the bottom of the windows. I will have to go back and check and put a bead there too. The screw holes is a good hypothesis. I had a similar thing happen in my house when they installed some new hurricane shutters. They did not caulk the screw holes into the cinder block and water leaked thru the holes, down thru the block and into the room. Caulking the holes solved the problem.
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