New players coming onto my server do not get put in the default group where I have permissions set up on my plugins. Therefore they think it is a vinilla server. I thought players coming in were automatically put in the defauult group. Any help would be appreciated.

That is handled automatically by Oxide each time the player connects. If they are not being added, then something is removing them else your server is unable to add them due to an error. Please test without any plugins and make sure to do a full reinstall with Oxide.

There are no known issues with the permission and group handling, which has been in place for years.