Tested the x64 exe. Everytime you launch arcade a mame.ini is generated in the root folder. Delete it and press F5 to refresh the list. Add a new rom folder and modify some setting. Close the emu and relaunch. A new mame.ini is generated again, but my settings are saved at ini/mame.ini correctly. The only problem is that ini generated everytime you launch arcade, but apart from this, all is going well.
Edit: The only thing I can't configure is to add a game to a custom folder, cause no folder is shown in the directory tree when the promp is opened.