Hmmmm, and you do not have any extra roms in the roms folder?
Also do not know if this is the issue, but you do not need slot0x25keysX.bin on your 3DS when using Derypt9 when you make your xorpads
Oh , ur right! there are some extra roms(No handled by ncchinfo_gen-exheader.py script) in the /roms folder. Good job , thx man!