Problem/Bug PermissionsEX won't let non-ops do anything

Hello,
I am starting a factions server with my friend, and currently having many problems with permissions.
1. The 'default' group cannot use /kit. I have tried adding different permissions nodes, nothing is working
2. The 'helper' group and above can't do anything like /kick, /mute, or /jail.
3. When I edit the permissions.yml from the console and not add permissions in-game, PermissionsEX often disables itself and I have to go back to a previous version of the file.
4. Nicknames do not appear in the chat at all.
I have not seen any errors in the start-up about PermissionsEX, so I have attached my permissions.yml file. Please help. I have tried using bPermissions, but the 'default' group is unable to do anything. I recently resetted the plugin by removing all of its files and reinstalling it.

Code:

groups:
  default:
    options:
      default: true
      prefix: '&7&l<&bMember&7&l>&r '
    permissions:
    - modifyworld.*
    - marry.*
    - essentials.msg
    - essentials.r
    - essentials.warp
    - essentials.warp.*
    - essentials.signs.use.*
    - essentials.money
    - essentials.baltop
    - essentials.tpa
    - essentials.tpaccept
    - essentials.tpdeny
    - essentials.tpahere
    - essentials.kits
    - essentials.kits.starter
    - essentials.home
    - essentials.spawn
    - essentials.sethome
    - essentials.delhome
    - essentials.mail
    - essentials.list
    - essentials.help
    - essentials.helpop
    - essentials.realname
    - essentials.suicide
    - factions.map
    - factions.desc
    - factions.neutral
    - factions.enemy
    - factions.ally
    - factions.show
    - factions.name
    - factions.join
    - factions.invite
    - factions.chat
    - factions.disband
    - factions.unsethome
    - factions.sethome
    - factions.create
    - factions.home
    - factions.title
    - factions.kick
    - factions.help
    - factions.promote
    - factions.demote
    - factions.officer
    - factions.claim
    - factions.unclaim
  helper:
    options:
      default: false
      prefix: '&8<&5&lHelper&8>&r '
      inheritance:
      - default
    permissions:
    - essentials.jail
    - essentials.unjail
    - essentials.kick
    - essentials.mute
    - essentials.unmute
    - essentials.togglejail
  mod:
    options:
      default: false
      prefix: '&7&l<&9Mod&7&l>&r '
      inheritance:
      - default
      - helper
    permissions:
    - essentials.chat.color
    - essentials.nick.color
    - essentials.fly
    - essentials.tempban
  builder:
    options:
      default: false
      prefix: '&7&l<&aBuilder&7&l>&r '
      inheritance:
      - default
    permissions:
    - minecraft.toggledownfall
    - voxelsniper.*
    - worldedit.*
    - essentials.gamemode.survival
    - essentials.gamemode.creative
    - essentials.gamemode
  admin:
    options:
      default: false
      prefix: '&7&l<&4Admin&7&l>&r '
      inheritance:
      - default
      - helper
      - mod
    permissions:
    - essentials.unban
    - essentials.ban
    - essentials.vanish
  dev:
    options:
      default: false
      prefix: '&7&l<&cDevelo&0p&cer&7&l>&r '
      inheritance:
      - default
      - helper
      - mod
      - admin
    permissions:
    - '*'
  manager:
    options:
      default: false
      prefix: '&7&l<&6Manager&7&l>&r '
    permissions:
    - '*'
  owner:
    options:
      default: false
      prefix: '&7&l<&9Owner&7&l>&r '
    permissions:
    - '*'