I only tested with PKM Gold (still downloading Layton's Mystery Journey right now), and my cia's checksum is matched as yours. So the cia is not corrupted.
The problem might be related to the "seed" like
@thom_tl said. Any games that require the firmware newer than 9.6 will need a "decryption seed" for them to work, otherwise those games will just freeze at boot screen, or "exception" will happen if using luma.
I don't know why I didn't need any other steps to get the game works. But try this:
* Uninstall and reinstall a game downloaded from villain3ds (example pkm gold) like normal.
* Try to open that game if you want. You will probably get the exception screen like usual.
* Restart the 3ds. Try to open the eShop, and go to that title page description (browse the page or search to find it).
* Go back to HOME menu and try to reopen that game.
If you can open the game after doing this then the decryption seed is the problem. I don't know why this is only happening with villain3ds. In that iso, chaos site those cia is already cryptofixed so it will work out of the box. About other apps like Wii U usb helper, maybe they are already included the seed with the cia pack (or cryptofixed it automatically) somehow.
Also, what version of FBI are you using to install those cias?