Basically, what is happening is I started a save with puzzles on, tried the first to pop up, found out I was going to run out of time, quit, then went into the settings and turned them off from the main menu. When I loaded the save, the puzzle still popped up as if I never set them to off. What I meant by whether it gets saved in the file as in the actual content save as opposed to a persistent or global save file that focuses on settings. I did run a test and I was apparently correct, it does save to the actual game save. I tested it by running it again without touching settings before loading, then went in once it was loaded and turned them off. That worked, confirming that the variable is maintained in the same file as the scenes themselves instead of a global dedicated file for settings.Im not sure what to answer on this because I've never tried it that way, so not sure what is going on.
It has to be on the savefile since its a variable being read after all.
Please, do try turning the puzzles on and off again, and you shouldn't have any issues.
OFF needs to be red, don't forget.