I had a look at the paper. So, stick to Floquet ports. The error your are getting usually happens when two or more dielectric is touching to a radiating surface, in this Zmin and Zmax. I don't see a reason why this should be the case for your geometry, so double check your model. Do you have anything placed on top of top dielectric surface (any vacuum box etc.)? If not, you may place a Vacuum Box to top and bottom to move your "Open" boundaries away from your dielectric substrate.
Another suggestion is to change "Open" radiating boundaries to "Open (add space)" boundaries. Because, if Open is chosen CST places PML to match the material touching to surface (as if those surfaces are extending to infinity), with "Open (add space)" it matches PML to Vacuum, so an infinite free space behavior is simulated.
There are two cases, one with the ground plane at the bottom. For the case with ground plane, you don't have to put any port to bottom, just assign Et = 0 boundary condition on that surface (i.e. right at the level where the ground plane is, you can adjust it with first putting a Vacuum box, and playing with height of it).