The Python scripts in 3DS Multi Decryptor work differently than the Python scripts in Decrypt9. It's good if it works that way, but somewhat tedious, right?
The seeddb.bin file (which is NOT the same as the 00000000 file) is meant to be a database of seeds. You put this database on your SD card once, and you don't have to fiddle around with the 00000000.sav file.
I'll take a look at ctrKeyGen.py. Maybe I can code a simple 00000000 -> seeddb.bin converter.
EDIT: I'm pretty sure I can quickly write that converter, but could you perhaps send me that seeddb / 00000000.sav file again? I only have it on my work computer now, to which I won't have access until tomorrow.
The 00000000 file from NAND\data\(console exclusive)\sysdata\0001000f holds all the seeds for all your games.I don't think there is a file named seeddb.bin in the nand unless you can extract it from the 00000000 file.
I'll send a pm with the 00000000.sav file.