Backup your emunand with EmuNandTool or other tools first.
Inject FBI, install FBI. Press L to NAND mode. Press R to remove title.
Iterate the whole title list, look for any titles whose titleid starting with 00040000 <- exactly this value only.
Those are SD app that should not be in NAND. Once find write down the titleid somewhere.
Then remove the title, when selecting it press A twice. All done? then reboot.
This issue is mainly caused by some SD apps inside your NAND/EmuNAND.