The options above didn't work for me, so I will describe my solution (Skyrim Special Edition): I had special character in my Windows username "C:/users/michał". Some programs can't handle the "ł", so they created another folder: "C:/users/michal". Skyrim launcher saves changes to .ini file in "michał", but the Skyrim actually uses the .ini file from "michal", so it doesn't see my changes to settings. If you think this is your case (you have some weird characters in your username), use the launcher to modify the settings as you want them to be (for example enable full screen) and save it. Then go to folder with the special character ("C:\Users\Michał\Documents\My Games\Skyrim Special Edition" in my case) and copy the .ini file to the folder without the special character ("C:\Users\Michal\Documents\My Games\Skyrim Special Edition"). If windows asks you to replace the file, accept it. Wasted 2 hours for that. I really have no idea why Windows allows for special characters in user names when it clearly leads to problems.
