Definition of "Port" as a boundary condition

I want to understand the definition of "Port" as a boundary condition in RF module.
Typical problem for setting Ports are shown in attached files (plasmonic_wire_grating.mph and plasmonic_wire_gratingMod.mph). Difference between these two files is only "Port". But results of transmission and reflection is quite different. What is the reason of this difference?

In my expectation, ports as a boundary condition determine the direction of poynting vector.