It is hard to diagnoise here without details of your settings. I would suggest that you manually setup a similar simple device and add the port exactly the same as you are currently using and check if it works. In principle FDTD can have mode source in xy,xz and yz plane without any issue for 3D simulation. Please check your simulation "dimension" to see if it is 2D and you add the mode source in xy plane. Before using advanced method please use simple way to verify the settings. If problem still exists, please post some screen copies here.
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