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Damian Marek

There are some things I would change, but the leading cause of the difference is that you are not simulating for enough time steps. The light gets trapped in the cavity and so you need to simulate long enough so most of the light has time to reach the output detector. Place an observation point at the same point as the transmission line (which I would make wider too) to see the convergence as is described in the example.

See the snapshot I took