Update: Thanks to everyone who insisted that my blackbox problem was indeed my problem i.e. titles installed to nand that shouldn't be there...
Anyways there is a quick 20min fix for this;
-back up problematic emunand using emunand tool
-find a spare mem card and inject problematic emunand to it, this mem card should have no Nintendo 3ds folder or a clean one
-use decrypt 9 to inject fbi to health and saftey in emunand
-use fbi emunand to install bigblue menu
-use bigblue menu to delete the CTR-x-xxxx files located on nand
-after a reboot check black box is gone and use decrypt 9 to restore health and safety app and use emunand tool again to move fixed emunand to problematic emunand card
By using a new card with a few Nintendo 3DS folder, the problematic files stick out like a sore thumb in BigBlue making it easier to identify
Thanks again ihaveamac.
Cheers