Boolean Union on Structure of Extruded Cubes failed Non Manifold Edges

no way to have the underside the exact shape as the upper side?
it worked like a charm on the rhino of my friend, even though the planes were in the same places

i created this file to better show my problem
structure.rar (11.2 MB)

i noticed my friend has no problems running all the commands and has no problems with overlapping surfaces (he uses rhino 5) anything that was changed which makes it complicated now?