Yes, Firmware Modifier is not 100% perfect. It will let you modify the settings, however with certain newer firmwares, it will wipe out "Games" etc... from your main menu. If that happens, STOP there and won't try it anymore. It's the way Firmware Modifier works. I've tried it on a few players and it wipes out my "Games" from the main menu too.
It's a pity because the Firmware Modifier can default our language to English, which is very handy esp if you're updating your firmware, then when u turn it on, it's all in Chinese. But after awhile u get to know the menus to change it back to English