I was hoping I'd find this link here. It never fails to deliver.
At this point, the term "CTR" has become a design smell.
On system start, the whole chunk is decrypted, the signature is verified, and everything works as expected. Until in the New 3DS, they decide to also additionally encrypt segment 3 (the ARM9 stuff) with a separate key on the NAND. That's what led to the whole mess. So I guess their mistaken assumption was that since FIRM was signed, the encrypted ARM9 section was protected. However, they didn't take account of the fact that the key to decrypt it can be corrupted. It's a bit subtle.
(I get that there are multiple ways to break a bug. :)