Running on CraftBukkit version git-Bukkit-b389396 (MC: 1.8)
Issue seams to be connected to PermissionsEx, EssentialsSpawn and Autorank
Plugins: Autorank v3.4 , PermissionsEx v1.23 and EssentialsSpawn vTeamCity(By the Spigot team)

Errors:

26.12 21:03:24 [Server] INFO at java.util.concurrent.FutureTask.run(Unknown Source) [?:1.7.0_03]
26.12 21:03:24 [Server] INFO at java.util.concurrent.FutureTask$Sync.innerRun(Unknown Source) [?:1.7.0_03]
26.12 21:03:24 [Server] INFO at java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source) [?:1.7.0_03]
26.12 21:03:24 [Server] INFO at net.minecraft.server.v1_8_R1.PacketHandleTask.run(SourceFile:13) [custom.jar:git-Bukkit-b389396]
26.12 21:03:24 [Server] INFO at net.minecraft.server.v1_8_R1.PacketPlayInClientCommand.a(SourceFile:8) [custom.jar:git-Bukkit-b389396]
26.12 21:03:24 [Server] INFO at net.minecraft.server.v1_8_R1.PacketPlayInClientCommand.a(SourceFile:31) [custom.jar:git-Bukkit-b389396]
26.12 21:03:24 [Server] INFO at net.minecraft.server.v1_8_R1.PlayerConnection.a(PlayerConnection.java:1283) [custom.jar:git-Bukkit-b389396]
26.12 21:03:24 [Server] INFO at net.minecraft.server.v1_8_R1.PlayerList.moveToWorld(PlayerList.java:448) [custom.jar:git-Bukkit-b389396]
26.12 21:03:24 [Server] INFO at net.minecraft.server.v1_8_R1.PlayerList.moveToWorld(PlayerList.java:508) [custom.jar:git-Bukkit-b389396]
26.12 21:03:24 [Server] INFO at org.bukkit.plugin.SimplePluginManager.callEvent(SimplePluginManager.java:486) [custom.jar:git-Bukkit-b389396]
26.12 21:03:24 [Server] INFO at org.bukkit.plugin.SimplePluginManager.fireEvent(SimplePluginManager.java:501) [custom.jar:git-Bukkit-b389396]
26.12 21:03:24 [Server] INFO at org.bukkit.plugin.RegisteredListener.callEvent(RegisteredListener.java:62) ~[custom.jar:git-Bukkit-b389396]
26.12 21:03:24 [Server] INFO at com.earth2me.essentials.spawn.EssentialsSpawn$1.execute(EssentialsSpawn.java:51) ~[?:?]
26.12 21:03:24 [Server] INFO at com.earth2me.essentials.spawn.EssentialsSpawnPlayerListener.onPlayerRespawn(EssentialsSpawnPlayerListener.java:65) ~[?:?]
26.12 21:03:24 [Server] INFO at com.earth2me.essentials.User.getGroup(User.java:670) ~[?:?]
26.12 21:03:24 [Server] INFO at com.earth2me.essentials.perm.PermissionsHandler.getGroup(PermissionsHandler.java:42) ~[?:?]
26.12 21:03:24 [Server] INFO at com.earth2me.essentials.perm.PermissionsExHandler.getGroup(PermissionsExHandler.java:23) ~[?:?]
26.12 21:03:24 [Server] INFO at ru.tehkode.permissions.PermissionManager.getUser(PermissionManager.java:171) ~[?:?]
26.12 21:03:24 [Server] INFO at ru.tehkode.permissions.bukkit.PermissionsEx.nameToUUID(PermissionsEx.java:356) ~[?:?]
26.12 21:03:24 [Server] INFO at org.bukkit.craftbukkit.v1_8_R1.CraftServer.getOfflinePlayer(CraftServer.java:1242) ~[custom.jar:git-Bukkit-b389396]
26.12 21:03:24 [Server] INFO at net.minecraft.server.v1_8_R1.UserCache.getProfile(SourceFile:118) ~[custom.jar:git-Bukkit-b389396]
26.12 21:03:24 [Server] INFO at net.minecraft.server.v1_8_R1.UserCache.c(SourceFile:170) ~[custom.jar:git-Bukkit-b389396]
26.12 21:03:24 [Server] INFO at net.minecraft.server.v1_8_R1.UserCache.a(SourceFile:186) ~[custom.jar:git-Bukkit-b389396]
26.12 21:03:24 [Server] INFO at com.google.common.collect.Lists.newArrayList(Lists.java:147) ~[custom.jar:git-Bukkit-b389396]
26.12 21:03:24 [Server] INFO at com.google.common.collect.Iterators.addAll(Iterators.java:357) ~[custom.jar:git-Bukkit-b389396]
26.12 21:03:24 [Server] INFO at com.google.common.collect.Iterators$9.next(Iterators.java:939) ~[custom.jar:git-Bukkit-b389396]
26.12 21:03:24 [Server] INFO at java.util.LinkedList$ListItr.next(Unknown Source) ~[?:1.7.0_03]
26.12 21:03:24 [Server] INFO at java.util.LinkedList$ListItr.checkForComodification(Unknown Source) ~[?:1.7.0_03]
26.12 21:03:24 [Server] INFO java.util.ConcurrentModificationException
26.12 21:03:24 [Server] ERROR Could not pass event PlayerRespawnEvent to EssentialsSpawn vTeamCity

26.12 21:05:34 [Server] INFO at org.bukkit.craftbukkit.v1_8_R1.scheduler.CraftAsyncTask.run(CraftAsyncTask.java:53)
26.12 21:05:34 [Server] INFO at org.bukkit.craftbukkit.v1_8_R1.scheduler.CraftTask.run(CraftTask.java:53)
26.12 21:05:34 [Server] INFO at me.armar.plugins.autorank.leaderboard.Leaderboard$2.run(Leaderboard.java:84)
26.12 21:05:34 [Server] INFO at me.armar.plugins.autorank.leaderboard.Leaderboard.updateLeaderboard(Leaderboard.java:185)
26.12 21:05:34 [Server] INFO at me.armar.plugins.autorank.leaderboard.Leaderboard.getSortedPlaytimes(Leaderboard.java:106)
26.12 21:05:34 [Server] INFO at net.milkbowl.vault.permission.Permission.playerHas(Permission.java:113)
26.12 21:05:34 [Server] INFO at net.milkbowl.vault.permission.plugins.Permission_PermissionsEx.playerHas(Permission_PermissionsEx.java:298)
26.12 21:05:34 [Server] INFO at net.milkbowl.vault.permission.plugins.Permission_PermissionsEx.getUser(Permission_PermissionsEx.java:247)
26.12 21:05:34 [Server] INFO at ru.tehkode.permissions.PermissionManager.getUser(PermissionManager.java:171)
26.12 21:05:34 [Server] INFO at ru.tehkode.permissions.bukkit.PermissionsEx.nameToUUID(PermissionsEx.java:356)
26.12 21:05:34 [Server] INFO at org.bukkit.craftbukkit.v1_8_R1.CraftServer.getOfflinePlayer(CraftServer.java:1242)
26.12 21:05:34 [Server] INFO at net.minecraft.server.v1_8_R1.UserCache.getProfile(SourceFile:118)
26.12 21:05:34 [Server] INFO at net.minecraft.server.v1_8_R1.UserCache.c(SourceFile:170)
26.12 21:05:34 [Server] INFO at net.minecraft.server.v1_8_R1.UserCache.a(SourceFile:186)
26.12 21:05:34 [Server] INFO at com.google.common.collect.Lists.newArrayList(Lists.java:147)
26.12 21:05:34 [Server] INFO at com.google.common.collect.Iterators.addAll(Iterators.java:357)
26.12 21:05:34 [Server] INFO at com.google.common.collect.Iterators$9.next(Iterators.java:939)
26.12 21:05:34 [Server] INFO at java.util.LinkedList$ListItr.next(Unknown Source)
26.12 21:05:34 [Server] INFO at java.util.LinkedList$ListItr.checkForComodification(Unknown Source)
26.12 21:05:34 [Server] INFO Caused by: java.util.ConcurrentModificationException
26.12 21:05:34 [Server] INFO at java.lang.Thread.run(Unknown Source)
26.12 21:05:34 [Server] INFO at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
26.12 21:05:34 [Server] INFO at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
26.12 21:05:34 [Server] INFO at org.bukkit.craftbukkit.v1_8_R1.scheduler.CraftAsyncTask.run(CraftAsyncTask.java:57)
26.12 21:05:34 [Server] WARN org.apache.commons.lang.UnhandledException: Plugin Autorank v3.4 generated an exception while executing task 81
26.12 21:05:34 [Server] WARN Exception in thread "pool-3-thread-8"

That's what I did write in top of the report.

Did you copy multiple errors? These are not very understable. Some errors are from Essentials.

I might found the cause:

02.01 02:32:38 [Server] INFO at org.bukkit.craftbukkit.v1_8_R1.scheduler.CraftAsyncTask.run(CraftAsyncTask.java:53)
02.01 02:32:38 [Server] INFO at org.bukkit.craftbukkit.v1_8_R1.scheduler.CraftTask.run(CraftTask.java:53)
02.01 02:32:38 [Server] INFO at me.armar.plugins.autorank.leaderboard.Leaderboard$3.run(Leaderboard.java:129)
02.01 02:32:38 [Server] INFO at me.armar.plugins.autorank.leaderboard.Leaderboard.updateLeaderboard(Leaderboard.java:185)
02.01 02:32:38 [Server] INFO at me.armar.plugins.autorank.leaderboard.Leaderboard.getSortedPlaytimes(Leaderboard.java:106)
02.01 02:32:38 [Server] INFO at net.milkbowl.vault.permission.Permission.playerHas(Permission.java:113)
02.01 02:32:38 [Server] INFO at net.milkbowl.vault.permission.plugins.Permission_PermissionsEx.playerHas(Permission_PermissionsEx.java:298)
02.01 02:32:38 [Server] INFO at net.milkbowl.vault.permission.plugins.Permission_PermissionsEx.getUser(Permission_PermissionsEx.java:247)
02.01 02:32:38 [Server] INFO at ru.tehkode.permissions.PermissionManager.getUser(PermissionManager.java:174)
02.01 02:32:38 [Server] INFO Caused by: java.lang.NullPointerException
02.01 02:32:38 [Server] INFO at java.lang.Thread.run(Unknown Source)
02.01 02:32:38 [Server] INFO at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
02.01 02:32:38 [Server] INFO at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
02.01 02:32:38 [Server] INFO at org.bukkit.craftbukkit.v1_8_R1.scheduler.CraftAsyncTask.run(CraftAsyncTask.java:57)
02.01 02:32:38 [Server] WARN org.apache.commons.lang.UnhandledException: Plugin Autorank v3.4 generated an exception while executing task 37785
02.01 02:32:38 [Server] WARN Exception in thread "pool-3-thread-7"

Happened when closing the server down.

It seems that Pex is having some problems getting the player, are you running the latest version?

Yes

Can you update to dev build 313? I changed code around for the leaderboard.

Would love to, but dev. server seams down

[18:47:28 ERROR]: Error occurred while enabling Autorank v3.4-Dev-317 (Is it up to date?)
java.lang.NullPointerException
at me.armar.plugins.autorank.config.ConfigHandler.getRequirements(ConfigHandler.java:128) ~[?:?]
at me.armar.plugins.autorank.playerchecker.builders.RankChangeBuilder.createFromAdvancedConfig(RankChangeBuilder.java:42) ~[?:?]
at me.armar.plugins.autorank.playerchecker.PlayerChecker.initialiseFromConfigs(PlayerChecker.java:179) ~[?:?]
at me.armar.plugins.autorank.Autorank.onEnable(Autorank.java:392) ~[?:?]
at org.bukkit.plugin.java.JavaPlugin.setEnabled(JavaPlugin.java:321) ~[craftbukkit.jar:git-Bukkit-5e6c347]
at org.bukkit.plugin.java.JavaPluginLoader.enablePlugin(JavaPluginLoader.java:327) [craftbukkit.jar:git-Bukkit-5e6c347]
at org.bukkit.plugin.SimplePluginManager.enablePlugin(SimplePluginManager.java:404) [craftbukkit.jar:git-Bukkit-5e6c347]
at org.bukkit.craftbukkit.v1_8_R1.CraftServer.loadPlugin(CraftServer.java:340) [craftbukkit.jar:git-Bukkit-5e6c347]
at org.bukkit.craftbukkit.v1_8_R1.CraftServer.enablePlugins(CraftServer.java:312) [craftbukkit.jar:git-Bukkit-5e6c347]
at net.minecraft.server.v1_8_R1.MinecraftServer.q(MinecraftServer.java:394) [craftbukkit.jar:git-Bukkit-5e6c347]
at net.minecraft.server.v1_8_R1.MinecraftServer.k(MinecraftServer.java:362) [craftbukkit.jar:git-Bukkit-5e6c347]
at net.minecraft.server.v1_8_R1.MinecraftServer.a(MinecraftServer.java:317) [craftbukkit.jar:git-Bukkit-5e6c347]
at net.minecraft.server.v1_8_R1.DedicatedServer.init(DedicatedServer.java:190) [craftbukkit.jar:git-Bukkit-5e6c347]
at net.minecraft.server.v1_8_R1.MinecraftServer.run(MinecraftServer.java:473) [craftbukkit.jar:git-Bukkit-5e6c347]
at java.lang.Thread.run(Thread.java:745) [?:1.8.0_25]

Can you show me your advancedconfig?

Used the new build you released and found the lines with the wrong code in. Thanks a lot!

Great!