Went through all the steps to make sure. Even wiped the server, and started with fresh download of mod. But nothing is protected. The /ao command shows player bases should be protected though. I'm not an expert on the hooks that aren't working right now, but does one of them affect this mod?

Here's the json config. Nothing changed there, has been working for months, until this Rust/Oxide update...

{
  "absoluteTimeScale": {},
  "activity": [
    "input",
    "loot",
    "respawn",
    "chat",
    "wakeup"
  ],
  "afkMinutes": 5,
  "clanFirstOffline": false,
  "clanShare": false,
  "cooldownMinutes": 6,
  "damageScale": {
    "1": 0.0,
    "12": 0.0,
    "3": 0.0,
    "24": 5.0,
    "6": 0.0
  },
  "interimDamage": 0.0,
  "minMembers": 1,
  "playSound": false,
  "prefabs": [
    "door.hinged",
    "door.double.hinged",
    "window.bars",
    "floor.ladder.hatch",
    "floor.frame",
    "wall.frame",
    "shutter",
    "wall.external",
    "gates.external",
    "box",
    "locker"
  ],
  "showMessage": true,
  "sound": "assets/prefabs/weapon mods/silencers/effects/silencer_attach.fx.prefab",
  "VERSION": "0.3.6"
}

On the server console run:

oxide.show perm antiofflineraid.protect

See if it's enabled for the group you want protected (server wide should be your default group).

For some reason when I ran the permissions after last wipe this one didn't take with the others. All is working now...

The permissions have to be there for this to work. Therefore, you will have to enter the permission in the server console. (Default is for everyone on the server. Do not use group default for admin only permissions).

oxide.grant group default antiofflineraid.protect
server.writecfg

Here is more info on permissions: https://umod.org/documentation/plugins/permissions