If you are in a subdomain whose web root is a subdirectory of your main site you will have to create this subdomain afresh and tell your hosting control panel to use a directory that's next to (above) your web root.
If you have already done so, please remember that the TLS (HTTPS) certificate for your main site will not cover this subdomain even if you are using a "star" certificate as you have two subdomain levels. You will have to set up a new TLS certificate for this subdomain.
If none of that helped, do remember that you do not need to run the Configuration Wizard. It's a convenience tool. You can simply try using the defaults in Akeeba Backup. Does the backup work with the defaults?
Nicholas K. Dionysopoulos
Lead Developer and Director
🇬🇷Greek: native 🇬🇧English: excellent 🇫🇷French: basic • 🕐 My time zone is Europe / Athens
Please keep in mind my timezone and cultural differences when reading my replies. Thank you!