Hey, so i got this on my server, and when any owners come online, they are automatically vanished, and since they don't know much about the plugins i get, they don't know to do /vanish to be able to talk again. I've looked in the config, but i cant figure out how to make it so that you aren't automatically vanished when you log on. Help?

If they're doing that, then you gave them the permission node for joining vanished. Read the permissions documentation :)

But the thing is they are an owner and their perms look like this:

Owner:
default: false
permissions:
- '*' <------------- Notice thats the only permission node..... that means perms to EVERYTHING
inheritance: []
info:
prefix: ''
build: true
suffix: ''

So i really cant edit their perms...

If you don't want to give them every single node then don't give them every single node.

But i DO want them to have every single node, just not logging on hidden... Nevermind. ill just go fix it in the .jar... Thanks for the idea anyways :/