Looking closely at the circles that did not appear as holes in the slab, 1 is a circular compex shape comprised of two arcs, this did form a hole in the created slab, 2 is a circular compex shape comprised of a single arc, this did not form a hole in the slab. 3 is a circle element added just for demonstration.
Were 1 and 2 drawn in ABD using the Arc tool instead of the Circle tool or were they imported from another format?