I’m sorry this is taking so long. The situation has become a bit more complicated. I just now got some time to fix the issues, and some of them are more involved than I thought. For some reason it is not saving any of the settings (hence restarting to the windowed mode. Settings are also reloaded when the menu is loaded, which is why that happens) and I cant figure out why.
I also cannot get this damn thing to run on Linux again after exporting. It keeps complaining about some libraries - that came packaged with the NWjs exec - being missing. I even put the libraries RIGHT NEXT TO THE PROGRAM and it still cant find it! I might roll the game back to its previous version until I look into this some more.