The characteristic line of empty brood cells is always along the line of the wire foundation. This effect disapears after the first round of brood rearing which makes me think that it is that the bees have had time to polish/ fill in the bottoms of the cells where the wire might be protruding. You also only see this on the side of the wax sheet that has been embedded (given that the wire has not penetrated right throught the mid rib) . Thats my theory of what is likely to be happenning - then again I may be wrong