your welcome
also i would like to take credit for this method you are referring to . . . lol before i realized the squares can be removed with bbm the advice being handed out in gbatemp was either
this problem can be caused a bug and/or user error (if caused by the bug then manually removing them may not work)
1. to restore the backup from before they existed
2. put them in a folder and ignore them
3. use this website
Title list - 3dbrew to verify what titles should be installed to sysnand destination nand and delete anything that does not compare properly in emunand destination nand (not safe in my opinion)
4. so after some trial and error when looking for a better cia installer (i hate fbi btw) i found that bbm only shows titles that have been added to the system (including legal eshop downloads) so the thing is if anything appears 2 or more times delete it bbm will only delete the copies and the black box will be gone
edit sorry forgot the website for method 3