Problem/Bug PEX Acting Strange

I have multiple servers all connected to MySQL and all work except one server and I do not know why.

I have deleted server, built back, removed plugins, add back plugins. It connects to the database, but the perms do not come through.

I do not understand why it is only partially working. Any suggestions I should check?

Code:

multiserver:
  use-netevents: true
permissions:
  backend: sql
  backends:
    sql:
      uri: mysql://ip.of.the.server/database
      user: username
      password: password
      type: sql
  basedir: plugins/PermissionsEx
  debug: false
  allowOps: false
  user-add-groups-last: false
  log-players: false
  createUserRecords: false
  informplayers:
    changes: false
updater: false
alwaysUpdate: false