the boundary conditions should be correct by now: Bloch in x- and y-direction and PML for both Zmin and Zmax. I also set the PML profile to stabilized rather than to standard. Decreasing the simulation to a value much smaller than default already improved my results, since now I'm able to recognize the bands which I expected to see. Why is this the case? However, my bandstructure still does not look clean.
Regarding the simulation status of the log files, I am not sure I completely got your point. All files terminate at 99% or 100%, so I don' think I need to resimulate any of them manually.
Please find attached the snapshot of the autoshutoff level and of the bandstructure.