You can't write to files in a zip folder. If you try to, it'll just create a new folder outside, and even then files in ZIP folders are read first (over ones in normal folders) if I remember correctly.
Either use RTB's system if the user has it (it already saves your prefs), or use a file stored in config/server if it doesn't. Write the default prefs to the file on the first run without RTB. This lets people edit the prefs easier, allows them to save correctly, supports RTB correctly and doesn't create unnecessary folders.