Bukkit

Describe to us the issue that you're having:
I will give a user a rank, do /perm save, /perm reload, and user loses rank I just gave them.

Which steps will reproduce this problem?:
1) /exec u:EpicRainbowPony a:setgroup v:observer
2) /perm save
3) cat /bPermissions/pml/users.yml
4) User is not saved in the users.yml file for my world pml.
5) /perm reload
6) EpicRainbowPony goes back to group default.
7) Error shows a random user jhco50, who is in my users.yml and states it's already defined! (Don't get that at all, as no changes were made to jhco50)
....

Do you have an error log of what happened?
[19:37:19] [Server thread/INFO]: nikitis issued server command: /perm reload
[19:37:20] [Server thread/WARN]: java.lang.IllegalArgumentException: The permission jhco50 is already defined!
[19:37:20] [Server thread/WARN]:        at org.bukkit.plugin.SimplePluginManager.addPermission(SimplePluginManager.java:599)
[19:37:20] [Server thread/WARN]:        at de.bananaco.bpermissions.imp.BukkitCompat.doBukkitPermissions(BukkitCompat.java:81)
[19:37:20] [Server thread/WARN]:        at de.bananaco.bpermissions.imp.BukkitCompat.setPermissions(BukkitCompat.java:38)
[19:37:20] [Server thread/WARN]:        at de.bananaco.bpermissions.imp.SuperPermissionHandler.setPermissions(SuperPermissionHandler.java:45)
[19:37:20] [Server thread/WARN]:        at de.bananaco.bpermissions.imp.SuperPermissionHandler.setupPlayer(SuperPermissionHandler.java:85)
[19:37:20] [Server thread/WARN]:        at de.bananaco.bpermissions.imp.YamlWorld.setupPlayer(YamlWorld.java:449)
[19:37:20] [Server thread/WARN]:        at de.bananaco.bpermissions.imp.YamlWorld.setupAll(YamlWorld.java:431)
[19:37:20] [Server thread/WARN]:        at de.bananaco.bpermissions.imp.Permissions.onCommand(Permissions.java:396)
[19:37:20] [Server thread/WARN]:        at org.bukkit.command.PluginCommand.execute(PluginCommand.java:44)
[19:37:20] [Server thread/WARN]:        at org.bukkit.command.SimpleCommandMap.dispatch(SimpleCommandMap.java:141)
[19:37:20] [Server thread/WARN]:        at org.bukkit.craftbukkit.v1_8_R3.CraftServer.dispatchCommand(CraftServer.java:641)
[19:37:20] [Server thread/WARN]:        at net.minecraft.server.v1_8_R3.PlayerConnection.handleCommand(PlayerConnection.java:1162)
[19:37:20] [Server thread/WARN]:        at net.minecraft.server.v1_8_R3.PlayerConnection.a(PlayerConnection.java:997)
[19:37:20] [Server thread/WARN]:        at net.minecraft.server.v1_8_R3.PacketPlayInChat.a(PacketPlayInChat.java:45)
[19:37:20] [Server thread/WARN]:        at net.minecraft.server.v1_8_R3.PacketPlayInChat.a(PacketPlayInChat.java:1)
[19:37:20] [Server thread/WARN]:        at net.minecraft.server.v1_8_R3.PlayerConnectionUtils$1.run(SourceFile:13)
[19:37:20] [Server thread/WARN]:        at java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source)
[19:37:20] [Server thread/WARN]:        at java.util.concurrent.FutureTask.run(Unknown Source)
[19:37:20] [Server thread/WARN]:        at net.minecraft.server.v1_8_R3.SystemUtils.a(SourceFile:44)
[19:37:20] [Server thread/WARN]:        at net.minecraft.server.v1_8_R3.MinecraftServer.B(MinecraftServer.java:715)
[19:37:20] [Server thread/WARN]:        at net.minecraft.server.v1_8_R3.DedicatedServer.B(DedicatedServer.java:374)
[19:37:20] [Server thread/WARN]:        at net.minecraft.server.v1_8_R3.MinecraftServer.A(MinecraftServer.java:654)
[19:37:20] [Server thread/WARN]:        at net.minecraft.server.v1_8_R3.MinecraftServer.run(MinecraftServer.java:557)
[19:37:20] [Server thread/WARN]:        at java.lang.Thread.run(Unknown Source)
[19:37:20] [Thread-10/INFO]: [bPermissions] Permissions for world pml has loaded!

Which version of bPermissions are you using?: (Please don't say "latest"!!!)
2.12 Beta 6
Which version of CraftBukkit?: (Please don't say "latest"!!!)
Spigot 1.8.8
Which OS?
CentOS 7
Any other information we may need (plugins, configs, etc):
EssentialsChat.  I've removed all other plugins for testing, but need this one for prefix's, and same result.

Please fill out this form properly! Failing to do so may result in your ticket being marked invalid.

I've been unable to reproduce this locally on my test server. It may be fixed in Beta 7, which is currently being reviewed by bukkitdev