I dont believe the issue HS directly but, indirectly. Often to get the clean close back to the frontend, it will force closes the emu which means any changes does not get saved. Open it with mame directly, change the dip switch and exit the emu properly. reopen it with mame to test that mame know where to save the cfg. if it did not save the changes, then go to the setting and make sure your directories are properly set up. Then try loading it through HS. If the issue is still there, then do the same thing, check the directories in the ahk file. If the issue is gone. then its golden