You will want use wave ports, not lumped ports. Lumped ports enforce a one volt drop along the rectangle. The problem you are solving is the coupling between two magnetic probes in a cavity. (If this does not make sense, let me know.)
To create the wave ports:
1.) select a face
2.) right mouse click, assign excitation
3.) define an impedance line from the bottom of the guide to the top
Changing to wave ports will yield a rectangular waveguide through-line. I ran this and got the expected S21 = 0dB.