I was able to fix this by placing another row of blocks under the outside wall, where in the picture the rooster was walking. I've also chiseled these, so it doesn't seem to be the chiseled blocks that were interfering with the chickens path finding, just the fact that the wall and floor were only diagonally adjacent to each other instead of being connected. Chickens can find their way inside now!
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M0th's post in my chickens cant find the way to their troughs and henboxes was marked as the answer