I would run that in a regular command prompt. Though it seems you're missing the certs filename in the bat-file. Add ie. ioFTPD.cer after -sy 12. And you might have to put a space between the CN part and "-eku".
Then it should generate a file called ioFTPD.cer that you have to install/import (double-click). You also have to change some things in your ioFTPD.ini, ie. removing a couple of # and ; so that those options are active.
Code:
### Encryption ###
Require_Encrypted_Auth = !*
Require_Encrypted_Data = !*
Certificate_Name = kebabfabriken
Explicit_Encryption = True
;Encryption_Protocol = TLS
Min_Cipher_Strength = 128
Max_Cipher_Strength = 256
/ZR