Thanks for sharing detailed results of your convergence tests! There could be a number of reasons why the FDTD and RCWA results don't match.
- Material Fitting: Both RCWA and FDTD use the multi-coefficient model for material fitting. I would recommend you to check the material fitting in both the cases to see how they compare.
- Mesh/k-vectors: You mentioned that the k-vectors do not affect the results, it can be because the structure does not need a large number of k-vectors and attains convergence with a small number. But, did you do convergence testing in FDTD wrt the mesh refinement? I am just curious about how confident you are about the FDTD results.
- Can you also check the index result in both FDTD and RCWA to see how the structure is resolved?
Sorry, I am not allowed to download any files, but would you be able to share screenshots of the simulation region in FDTD and the screenshots of Mesh Settings and Boundary Conditions Tab of FDTD?