Changing S parameters

I am calculating and then plotting the reflection and transmission coefficients [abs(S11)^2 and abs(S21)^2] for a plasmonic wire grating structure using the RF module. Initially I set the ports at a distance of 1.5 times the maximum wavelength from the grating. In second simulation I then moved the ports further away to a distance of 2.5 times the maximum wavelength from the grating. The 1D reflection and transmission coefficients plot changes substantially.

Are there standing wave effects coming into play between the grating and ports? Is there some type of isolator that I should be using to make sure the radiation travels in only one direction?

v/r

John