There are a few reasons for not having 100% transmission:
1: the moitors do not enclose a complete box to cover the whole device
2:the source mode might be cut
3: discrete error from simulation. you may reduce this by increasing the mesh accuracy
4: the simulation time is not long enough, or the autoshutoff min is not small enough as now it is a cavity with multiple reflections.
Please also check if there is any material loss. One more: do you add the total powers from the ports, or just use abs(S)^2? when there is abruption of the waveguides, it can excite higher-order of modes. You should use the total power from the ports. I believe that you calcualted the total power from other monitors.
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