I would not expect both the structures to have the same response as the unit cell geometry is different in each case (for ex. the periodicity of the two geometries is different). But the second graph is clearly not accurate. It is possible that the structure needs more k-vectors to obtain convergence. I would ask you to increase the number of k-vectors (max number of ku and kv vectors in the Solver tab of RCWA) and see if you see any improvements.
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