Alright, so here's what I've done. (No other mods installed, though I ran mods though V11, but that's all deleted and gone.)
With the standard scripts.rxdata that you just sent me, the game loads and works fine. Soft resetting and closing/reopening the game has no problems at all.
When I replace it with the scripts.rxdata in post 2, I get the same result: Debug works fine and I can change whatever I wish (This time I didn't change anything.) Game saves fine.
I did notice though that a new filed labelled "PBS" appears in the Rejuvenation - V12 folder as well