1.7.2 Pixelmon Help (Permissions)

I have been having some problems with permissions
Now I don't specifically know why the permissions aren't working
but the commands only work if you are opped
you will recieve the ussual message "You do not have access to that command"

here is the control panel
06.08 02:11:11 [Server] INFO You can disable automatic update checking in the config.
06.08 02:11:11 [Server] INFO Visit http://dev.bukkit.org/bukkit-plugins/voteroulette/
06.08 02:11:11 [Server] INFO There's a different version available: 2.3.2 (Current version is: 2.0.3)
06.08 02:11:10 [Server] WARN Update at: http://dev.bukkit.org/server-mods/vault
06.08 02:11:10 [Server] WARN Stable Version: 1.4.1 is out! You are still running version: 1.2.31
06.08 02:11:10 [Server] INFO Checking for Updates:
06.08 02:11:09 [Server] INFO at java.lang.Thread.run(Unknown Source) [?:1.7.0_01]
06.08 02:11:09 [Server] INFO at net.minecraft.server.MinecraftServer.run(MinecraftServer.java:614) [MinecraftServer.class:?]
06.08 02:11:09 [Server] INFO at net.minecraft.server.MinecraftServer.func_147138_a(MinecraftServer.java:744) [MinecraftServer.class:?]
06.08 02:11:09 [Server] INFO java.lang.NullPointerException
06.08 02:11:09 [Server] ERROR Couldn't load server icon
06.08 02:11:09 [Server] INFO Registered command pokebattle2 with permission node com.pixelmonmod.pixelmon.commands.Battle2
06.08 02:11:09 [Server] INFO Registered command resetpokestats with permission node com.pixelmonmod.pixelmon.commands.StatsReset
06.08 02:11:09 [Server] INFO Registered command pokestats with permission node com.pixelmonmod.pixelmon.commands.Stats
06.08 02:11:09 [Server] INFO Registered command pokegive with permission node com.pixelmonmod.pixelmon.commands.PokeGive
06.08 02:11:09 [Server] INFO Registered command pokebattle with permission node com.pixelmonmod.pixelmon.commands.Battle
06.08 02:11:09 [Server] INFO Registered command pokeheal with permission node com.pixelmonmod.pixelmon.commands.Heal
06.08 02:11:09 [Server] INFO Registered command freeze with permission node com.pixelmonmod.pixelmon.commands.Freeze
06.08 02:11:09 [Server] INFO Registered command struc with permission node com.pixelmonmod.pixelmon.commands.Struc
06.08 02:11:09 [Server] INFO Registered command pokespawn with permission node com.pixelmonmod.pixelmon.commands.Spawn
06.08 02:11:09 [Server] INFO Registered command forge with permission node net.minecraftforge.server.command.ForgeCommand
06.08 02:11:09 [Server] Startup Done (11.353s)! For help, type "help" or "?"
06.08 02:11:09 [Server] INFO Server permissions file permissions.yml is empty, ignoring it
06.08 02:11:09 [Server] INFO Votifier plugin found, enabling Votifier support.
06.08 02:11:09 [Server] INFO MC 1.7.9 or below found, enabling version 1 player handling.
06.08 02:11:09 [Server] INFO MC 1.7.2 or above found, enabling version 2 log handling.
06.08 02:11:09 [Server] INFO MC 1.3 or above found, enabling version 2 XP handling.
06.08 02:11:09 [Server] INFO Enabling EnjinMinecraftPlugin v2.6.8
06.08 02:11:09 [Server] INFO Enabling EssentialsChat v2.13.1
06.08 02:11:09 [Server] WARN There is a new version of ChestShop available, however it is only compatible with Minecraft 1.7.8 and higher!
06.08 02:11:09 [Server] WARN There is a new version of ChestShop available, however it is only compatible with Minecraft 1.7.8 and higher!
06.08 02:11:09 [Server] WARN There is a new version of ChestShop available, however it is only compatible with Minecraft 1.7.8 and higher!
06.08 02:11:09 [Server] INFO Vault loaded! Found an economy plugin!
06.08 02:11:09 [Server] INFO LWC version 4.4.0 (b881) (July 11, 2013) loaded.
06.08 02:11:09 [Server] WARN java.lang.UnsatisfiedLinkError: Native Library /plugins/LWC/lib/native/Linux/amd64/libsqlitejdbc.so already loaded in another classloader
06.08 02:11:09 [Server] INFO Enabling ChestShop v3.7.9
06.08 02:11:09 [Server] INFO 2 - Portals(s) loaded
06.08 02:11:08 [Server] INFO - Version 2.5-b699 Enabled - By Rigby and fernferret
06.08 02:11:08 [Server] INFO Enabling Multiverse-Portals v2.5-b699
06.08 02:11:08 [Server] INFO Enabling EssentialsSpawn v2.13.1
06.08 02:11:08 [Server] INFO =============================================================
06.08 02:11:08 [Server] INFO Version: 0.88.0.0_(1.7.2) - Mod Enabled
06.08 02:11:08 [Server] INFO =============================================================
06.08 02:11:08 [Server] INFO Time until a New Day: 9 hours, 48 minutes, 52 seconds
06.08 02:11:08 [Server] INFO Using: PermissionsEX v1.21.3, Vault v1.2.31-b411
06.08 02:11:08 [Server] WARN Check your CraftBukkit version as we do not test on custom/old builds.
06.08 02:11:08 [Server] WARN Towny requires version 2918 or higher.
06.08 02:11:08 [Server] WARN Unable to read CraftBukkit Version.
06.08 02:11:08 [Server] INFO Database: [Load] flatfile [Save] flatfile
06.08 02:11:08 [Server] INFO ==================== Towny ========================
06.08 02:11:08 [Server] INFO Enabling Towny v0.88.0.0_(1.7.2)
06.08 02:11:08 [Server] INFO Payment method found (Vault - Economy: iConomy 7 version: 1.2.31-b411)
06.08 02:11:08 [Server] INFO Essentials: Using PermissionsEx based permissions.
06.08 02:11:08 [Server] INFO [Vault][Economy] Essentials Economy hooked.
06.08 02:11:07 [Server] INFO 1.7.2-R0.4-SNAPSHOT
06.08 02:11:07 [Server] INFO git-Cauldron-MCPC-Plus-1.7.2-1.1147.04.84 (MC: 1.7.2)
06.08 02:11:07 [Server] INFO Bukkit version format changed. Version not checked.
06.08 02:11:07 [Server] INFO Enabling Essentials v2.13.1
06.08 02:11:07 [Server] INFO Votifier enabled.
06.08 02:11:07 [Server] INFO Enabling Votifier v1.9
06.08 02:11:07 [Server] INFO Version 2.5-b678 (API v18) Enabled - By Rigby, fernferret, lithium3141 and main--
06.08 02:11:07 [Server] INFO 4 - World(s) loaded.
06.08 02:11:07 [Server] WARN An update to PermissionsEx version 1.22.1 is available to download from http://dev.bukkit.org/bukkit-plugins/permissionsex/. Please review the changes and update as soon as possible!
06.08 02:11:07 [Server] INFO No updates found!
06.08 02:11:07 [Server] INFO Loaded configuration for world 'spawn'
06.08 02:11:07 [Server] INFO (spawn) Fire spread is UNRESTRICTED.
06.08 02:11:07 [Server] INFO (spawn) Lava fire is blocked.
06.08 02:11:07 [Server] INFO (spawn) Lighters are PERMITTED.
06.08 02:11:07 [Server] INFO (spawn) TNT ignition is PERMITTED.
06.08 02:11:07 [Server] INFO Preparing start region for level 3 (Dimension: 2, Seed: 6573684221381187691)
06.08 02:11:07 [Server] INFO Loading dimension 2 (spawn) (net.minecraft.server.dedicated.DedicatedServer@407964d6)
06.08 02:11:07 [Multicraft] Skipped 12 lines due to rate limit (30/s)
06.08 02:11:06 [Server] INFO No config updates found...
06.08 02:11:05 [Server] INFO Loading modules...
06.08 02:11:05 [Server] INFO Enabling ClearLag v2.7.1
06.08 02:11:05 [Server] INFO CompatNoCheatPlus v6.4.4-RC-sMD5NET-b61 is enabled. Some hooks might get registered with NoCheatPlus later on.
06.08 02:11:05 [Server] ERROR Plugin CompatNoCheatPlus v6.4.4-RC-sMD5NET-b61 has failed to register events for class me.asofold.bpl.cncp.hooks.generic.HookBlockPlace because fr/neatmonster/nocheatplus/checks/CheckType does not exist.
06.08 02:11:05 [Server] ERROR Plugin CompatNoCheatPlus v6.4.4-RC-sMD5NET-b61 has failed to register events for class me.asofold.bpl.cncp.hooks.generic.HookBlockBreak because fr/neatmonster/nocheatplus/checks/CheckType does not exist.
06.08 02:11:05 [Server] ERROR Plugin CompatNoCheatPlus v6.4.4-RC-sMD5NET-b61 has failed to register events for class me.asofold.bpl.cncp.hooks.generic.HookInstaBreak because [Lfr/neatmonster/nocheatplus/checks/CheckType; does not exist.
06.08 02:11:05 [Server] INFO Registered hook(NCPHook might get added later): InstaBreak(default) / 1.0
06.08 02:11:05 [Server] INFO Registered hook(NCPHook might get added later): BlockPlace(default) / 1.0
06.08 02:11:05 [Server] INFO Registered hook(NCPHook might get added later): BlockBreak(default) / 1.1
06.08 02:11:05 [Server] INFO Ensured that the following plugin is enabled: WorldGuard
06.08 02:11:05 [Server] INFO 0 regions loaded for 'DIM-1'
06.08 02:11:05 [Server] INFO 0 regions loaded for 'DIM1'
06.08 02:11:05 [Server] INFO 1 regions loaded for 'LostLegacy'
06.08 02:11:05 [Server] INFO Loaded configuration for world 'DIM-1'
06.08 02:11:05 [Server] INFO (DIM-1) Fire spread is UNRESTRICTED.
06.08 02:11:05 [Server] INFO (DIM-1) Lava fire is blocked.
06.08 02:11:05 [Server] INFO (DIM-1) Lighters are PERMITTED.
06.08 02:11:05 [Server] INFO (DIM-1) TNT ignition is PERMITTED.
06.08 02:11:05 [Server] INFO Loaded configuration for world 'DIM1'
06.08 02:11:05 [Server] INFO (DIM1) Fire spread is UNRESTRICTED.
06.08 02:11:05 [Server] INFO (DIM1) Lava fire is blocked.
06.08 02:11:05 [Server] INFO (DIM1) Lighters are PERMITTED.
06.08 02:11:05 [Server] INFO (DIM1) TNT ignition is PERMITTED.
06.08 02:11:05 [Server] INFO Loaded configuration for world 'LostLegacy'
06.08 02:11:05 [Server] INFO (LostLegacy) Fire spread is UNRESTRICTED.
06.08 02:11:05 [Server] INFO (LostLegacy) Lava fire is blocked.
06.08 02:11:05 [Server] INFO (LostLegacy) Lighters are PERMITTED.
06.08 02:11:05 [Server] INFO (LostLegacy) TNT ignition is PERMITTED.
06.08 02:11:05 [Server] INFO Enabling WorldGuard v5.9
06.08 02:11:05 [Multicraft] Skipped 11 lines due to rate limit (30/s)
06.08 02:11:05 [Server] INFO Enabling iConomy v7.0
06.08 02:11:05 [Server] INFO Enabling AutoBroadcaster v0.4
06.08 02:11:05 [Server] INFO WEPIF: Using the Bukkit Permissions API.
06.08 02:11:05 [Server] INFO Enabling WorldEdit v5.6
06.08 02:11:05 [Server] INFO Enabled!
06.08 02:11:04 [Server] INFO ...finished loading configs!
06.08 02:11:04 [Server] WARN Your milestone section is empty, no milestones will be given!
06.08 02:11:04 [Server] INFO Added Reward: This Could be Useful
06.08 02:11:04 [Server] WARN The Reward "This Could be Useful" appears to be empty. Check your config settings!
06.08 02:11:04 [Server] INFO Added Reward: Get yourself Something good
06.08 02:11:04 [Server] WARN The Reward "Get yourself Something good" appears to be empty. Check your config settings!
06.08 02:11:04 [Server] INFO Added Reward: Pokemon Love These
06.08 02:11:04 [Server] WARN The Reward "Pokemon Love These" appears to be empty. Check your config settings!
06.08 02:11:04 [Server] INFO Added Reward: Diaminds Priceless
06.08 02:11:04 [Server] INFO "Gotta Catchem All" saved as default reward.
06.08 02:11:04 [Server] INFO Added Reward: Gotta Catchem All
06.08 02:11:04 [Server] WARN The Reward "Gotta Catchem All" appears to be empty. Check your config settings!

here is the PermissionsEx File
groups:
Member:
default: true
Permissions:
- essentials.help
- essentials.home
- essentials.warp
- essentials.sethome
- essentials.remhome
- essentials.rules
- essentials.back
- essentials.ignore
- essentials.msg
- essentials.tpa
- essentials.tpahere
- essentials.tpaccept
- essentials.tpdeny
- essentials.warp.list
- essentials.spawn
- essentials.mail
- towny.wild.build.*
- towny.wild.destroy.*
- towny.wild.switch.*
- towny.wild.item_user.*
BuildTeam:
default: false
Permissions:
- worldedit.*
- worldguard.*
- essentials.gamemode
- essentials.effect
- essentials.speed
- essentials.help
- essentials.home
- essentials.warp
- essentials.sethome
- essentials.remhome
- essentials.rules
- essentials.back
- essentials.ignore
- essentials.msg
- essentials.tpa
- essentials.tpahere
- essentials.tpaccept
- essentials.tpdeny
- essentials.warp.list
- essentials.spawn
- essentials.mail
- towny.wild.build.*
- towny.wild.destroy.*
- towny.wild.switch.*
- towny.wild.item_user.*
- essentials.heal
- essentials.workbench
- essentials.fly
- essentials.feed
Helper:
default: false
Permissions:
- essentials.heal
- essentials.workbench
- essentials.fly
- essentials.feed
- essentials.help
- essentials.home
- essentials.warp
- essentials.sethome
- essentials.remhome
- essentials.rules
- essentials.back
- essentials.ignore
- essentials.msg
- essentials.tpa
- essentials.tpahere
- essentials.tpaccept
- essentials.tpdeny
- essentials.warp.list
- essentials.spawn
- essentials.mail
- towny.wild.build.*
- towny.wild.destroy.*
- towny.wild.switch.*
- towny.wild.item_user.*
Moderator:
Default: false
Permissions:
- essentials.ban
- essentials.fly
- essentials.mute
- essentials.tempban
- essentials.time
- essentials.help
- essentials.home
- essentials.warp
- essentials.sethome
- essentials.remhome
- essentials.rules
- essentials.back
- essentials.ignore
- essentials.msg
- essentials.tpa
- essentials.tpahere
- essentials.tpaccept
- essentials.tpdeny
- essentials.warp.list
- essentials.spawn
- essentials.mail
- towny.wild.build.*
- towny.wild.destroy.*
- towny.wild.switch.*
- towny.wild.item_user.*
- essentials.heal
- essentials.workbench
- essentials.fly
- essentials.feed
VIP:
default: false
permissions:
- essentials.fly
- essentials.gamemode
- essentials.tp
- essentials.tphere
- essentials.me
- essentials.nick
GymLeader:
Default: false
permissions:
- essentials.tp
- essentials.tphere
- essentials.fly
- essentials.me
- essentials.suicide
inheritence:
- Member
- VIP
- Helper
Admin:
Default: false
Permissions:
- essentials.banip
- essentials.gamemode
- logblock.*
- pex.*
inheritence:
- Member
- Moderator
- Helper
Co-Owner:
Default: false
Permissions:
- '*'
Owner:
Default: false
permissions:
- '*'
schema-version: 1
users:
77199f5c-f2bb-447a-8906-fb8053d38798:
group:
- Co-Owner
options:
name: xTheWiseONe
xtheiwseone:
group:
- GymLeader
9297f4ab-d84b-46ce-a049-d5058593be8d:
group:
- BuildTeam
options:
name: alecpersse
7a7573ca-4169-47ce-bce1-9f1fc89124d6:
group:
- Owner
options:
name: everydaylol
2c202e32-4d6f-4cbe-b1a9-a7809f4b3c0d:
group:
- Admin
options:
name: _ShiftyG
7fb1453a-d4f9-45e5-b84c-fc2c086de03d:
group:
- Moderator
options:
name: 1nightshot1

 

Locked. Please seek support where you found the mod you use. We are unable to support any software other than Bukkit/CraftBukkit.