OK, well it wasn't so black & white after all unfortunately. It seems my monitor (or the Ratte switch) does not like Indivision settings where you Override Limits. These modes somehow test fine in the Indivision config tool but don't work when e.g. WHDLoad switches to such a e.g. PAL the screen is switched but stays black or is not even switched.
So for now I'm staying with a nearly default PAL config. This works OK, at 60Hz unfortunately an most annoyingly has those lines cut off from the top and bottom. I never really managed to get these missing lines back. Especially now where I cannot enable Override Limits.