What menuhax are you using? I use menuhax, but it doesn't do anything unless I hold L when I power on the console...Are your sysNand and emuNand Linked? If so that's the issue. You need to format sysNand to remove the link and reinstall ThemeHax. Just remove the SD card and boot up the 3DS and do the System Format.
Almost forgot, you have to remove MenuHax first by deleting the Themes Folder on the SD card. Otherwise when you load emuNand it will load MenuHax. Changing the Theme while in sysNand before formatting should remove it also. If you use the 2nd method, you have to re-create emuNand.












