
So if this problem hits someone else then this is how it can be fixed. Today it all works as it should regarding the mysterious checkbox problem. The other bug with MO not caring if i unselected a mod or not is also gone, but that was most likely due to some bug related to running the MO and continuously making changes for about 10+ hours without any reboot or restart of the program. I solved it by adding the missing "bLoad." entry in the ini-file and THEN setting the ini-file to Read Only, reasoning that it might prevent MO from making whatever reverting to older state it was doing and VOILA! That worked, now faces match the body and the entry stays in the ini-file.

They disappear if i uninstall them but simply unchecking the checkbox seems to do nothing. I also unchecked some other plugins but once i start the game they are still active. The ini file changes back to its former state every time i start the game with NVSE. DO NOT USE ANYTHING FROM THE WINDOWS APP STORE. Having trouble extracting the archive Install via Steam, use the installer, or download 7-zip. "Perhaps I did not remember to save" was my thought so I did the change again. Current SE build 2.0.20 (runtime 1.5.97): 7z archive. Went back to the Ini file and the change i had made was gone. So i made the relevant change but when i started the game again I still had the problem.

I remembered that the problem usually was the "bLoad." line in the ini file and sure enough it was missing. But then last night i got the "white faces on black body" bug. SO, i have been modding away (Mod Organizer 2) for about 10 hours now, periodically started the game to check that all works.
