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Spoiler alert - text in white below
Its an optical illusion - the slope of the red triangle and the slop of the green triangle are not the same. In the top configuration they go slightly "concave", in the bottom they go slightly "convex" - the difference between the two is 1 square's worth.
Thanks all, it's mathematically sound. But that still doesn't explain why I can cut these shapes out of graph paper (and using a straight edge to draw the hypotenuse) and duplicate the 'hole'.