Ok, so here's my experience with starting a new game:
I see all the screens, everything looks fine, key config is possible BUT the following options i tested and were not saved (everything else, like health generation and stuff now works though):
- Extra WP per level
- Simple loot system
- % of Dodge for Athletics
- % of Ironskin Damage reduction.
I did not test the other options at the end of the menu, cause those were the 4 i wanted to change and that did not work.
So in short: Starting a new character helped with most things and now i can play it since the health regeneration is at a reasonable amount and the key configuration works too, BUT the 4 mentioned options (probably alongside the others in that menu, i didn't test), still won't save when i leave the "Mod Options" screen.
Don't know if i missed it, but i did not see any incompatibility disclaimer with the Floris expanded savegames, so maybe if I'm not blind you could add that in the first post, to keep people like me from asking why it doesn't work
So thanks again for the improvements and the reply, maybe my report up there helps you in finding the issue