Sinusoidal corrugated waveguide problem in HFSS

I am designing an infinite corrugated waveguide whose its walls are sinusoidal corrugated in order to get the*filtering response. I have assigned perfect electric boundaries to its walls as well as wave ports. The figures I have got in HFSS have the same shape with those I have got in MATLAB but with a shift in resonance frequency. Also, when choosing delta (which is the corrugation amplitude) less than 0.1, it does not work correctly. Is the problem in the boundary and ports assignment? and what is the suggested solution for this?