I'm currently using the Permissions addon, but since I'm the server owner, the * permission should allow me to properly use the /region command anyways. My issue is that even if I have an area selected, the /region command does not work for me.

I type it like this:

/region define Spawn Winguh

Is that correct?

That's correct. Does it say that it's using Permissions on server boot up?

I'm running it with a website host, so I don't have a GUI, could I instead try to delete Permissions and see if that works instead?

The server generates .log files I think.

Ask on forum / new issue tracker.