Hooray it just wasn't me! So just to recap
@motezazer @d0k3 if I was to say download it again on 10.x and then generate everything all over again it would work and it was just the version I personally captured that has since been updated and that version work?
Correct, it would work.
The explanation for the failing decryption of some newer N3DS only eShop titles, which
@Shadowtrance and
@OctopusRift will be interested in is as follows...
There's a new kind of encryption called the Secure4 encryption. This can, for some reason, only be used for N3DS only eShop titles. Secure4 encryption uses new keys for several keyslots. Without the keys (which can, if even possible, only be acquired by someone with some serious hacking skills), Secure4 encrypted titles can only be decrypted on N3DS consoles >= FW 9.6. If you followed this thread closely and / or have a basic understanding of how these things work, you understand the catch by now:
We cannot run Decrypt9 on consoles > 9.2 and we cannot decrypt Secure4 on consoles < 9.6. In short: Secure4 cannot be decrypted yet.
Luckily, only very few titles are Secure4 encrypted by now, and as I said, it is limited to N3DS only eShop titiles. The first release of Binding of Isaac Afterbirth had Secure4 encryption, after the update (ie. with the version now downloadable from the eShop), Secure4 encryption is strangely gone. Animal Crossing: Happy Home Designer seems to have Secure4 encryption, too (needs confirmation).
Now, what to do about that? I'm assuming that if ncchflag[3] == 0x0B, Secure4 is used (it was ncchflag[3] == 0x0A for Secure3).
Here is the explanation of the NCCH header. I do now check for that (in both, NCCH padgen and the title decryptor), and if Secure4 is detected, you at least get a proper error message instead of inexplainable problems.
If anyone can add some useful info to this, or even better, tell me that I'm wrong, your participation is greatly appreciated.