2013-07-07 16:04:21 [INFO] [TickThreading] Started TT metrics reporting. This can be disabled in PluginMetrics.cfg
2013-07-07 16:04:39 [INFO] [TickThreading] Threading initialised for world Promised Land/20
2013-07-07 16:04:39 [INFO] [TickThreading] Threading initialised for world Twilight Forest/7
2013-07-07 16:04:39 [INFO] [TickThreading] Threading initialised for world Wyvern Lair/-17
2013-07-07 16:04:39 [INFO] [TickThreading] Threading initialised for world The End/1
2013-07-07 16:04:39 [INFO] [TickThreading] Threading initialised for world Nether/-1
2013-07-07 16:04:39 [INFO] [TickThreading] Threading initialised for world Overworld/0
2013-07-07 16:04:44 [SEVERE] [TickThreading] TickThreading v1.5.2.94 for MC1.5.2 on 1.5.2 tickthreading,mcpc,spigot,craftbukkit,forge,fml - 1.7.0_25-b16 is installed on this server!
If anything breaks, check if it is still broken without TickThreading
We don't want to annoy mod devs with issue reports caused by TickThreading.
Seriously, please don't.
If it's only broken with TickThreading, report it at http://github.com/nallar/TickThreading

Also, you really should be making regular backups. (You should be doing that even when not using TT.)
2013-07-07 16:09:41 [SEVERE] [TickThreading] Exception ticking TileEntity c JAKJ.RedstoneInMotion.CarriageEngineEntity @1252852893 in Overworld/0 at x, y, z: -203, 66, -75
java.lang.IllegalAccessError
	at JAKJ.RedstoneInMotion.NbtCompound.<init>(NbtCompound.java:17)
	at JAKJ.RedstoneInMotion.TileEntity.func_70310_b(TileEntity.java:36)
	at JAKJ.RedstoneInMotion.CarriageEntity.func_70310_b(CarriageEntity.java:78)
	at JAKJ.RedstoneInMotion.CarriagePackage.AddBlock(CarriagePackage.java:100)
	at JAKJ.RedstoneInMotion.PlatformCarriageEntity.FillPackage(PlatformCarriageEntity.java:23)
	at JAKJ.RedstoneInMotion.CarriageEngineEntity.GeneratePackage(CarriageEngineEntity.java:17)
	at JAKJ.RedstoneInMotion.CarriageDriveEntity.BeginMotion(CarriageDriveEntity.java:227)
	at JAKJ.RedstoneInMotion.CarriageDriveEntity.func_70316_g(CarriageDriveEntity.java:210)
	at nallar.tickthreading.minecraft.tickregion.TileEntityTickRegion.doTick(TileEntityTickRegion.java:100)
	at nallar.tickthreading.minecraft.tickregion.TickRegion.run(TickRegion.java:35)
	at nallar.tickthreading.minecraft.ThreadManager$2.run(ThreadManager.java:101)
	at nallar.tickthreading.minecraft.ThreadManager$1.run(ThreadManager.java:43)
	at nallar.tickthreading.util.FakeServerThread.run(FakeServerThread.java:16)
2013-07-07 16:12:04 [WARNING] [TickThreading] Unsafe entity list iteration
java.lang.Throwable
	at nallar.tickthreading.minecraft.entitylist.EntityList.iterator(EntityList.java:72)
	at mithion.arsmagica.AMCore.onPlayerLogout(AMCore.java:525)
	at cpw.mods.fml.common.registry.GameRegistry.onPlayerLogout(GameRegistry.java:14)
	at net.minecraft.server.management.ServerConfigurationManager.disconnect(ServerConfigurationManager.java:389)
	at net.minecraft.network.NetServerHandler.func_72515_a(NetServerHandler.java:956)
	at net.minecraft.network.TcpConnection.func_74428_b(TcpConnection.java:449)
	at net.minecraft.network.NetServerHandler.func_72570_d(NetServerHandler.java:222)
	at net.minecraft.network.NetworkListenThread.b_net_minecraft_network_NetworkListenThread_networkTick_p0(NetworkListenThread.java:53)
	at net.minecraft.network.NetworkListenThread.func_71747_b(NetworkListenThread.java)
	at net.minecraft.server.dedicated.DedicatedServerListenThread.func_71747_b(SourceFile:30)
	at net.minecraft.server.MinecraftServer.func_71190_q(MinecraftServer.java:431)
	at net.minecraft.server.dedicated.DedicatedServer.func_71190_q(DedicatedServer.java:320)
	at net.minecraft.server.MinecraftServer.func_71217_p(MinecraftServer.java:303)
	at net.minecraft.server.MinecraftServer.run(MinecraftServer.java:195)
	at net.minecraft.server.ThreadMinecraftServer.run(SourceFile:573)
2013-07-07 16:12:13 [INFO] [TickThreading] Server shutting down - requested at
nallar.insecurity.ThisIsNotAnError: This is not an error.
	at nallar.insecurity.InsecurityManager.checkExit(InsecurityManager.java:31)
	at net.minecraft.server.MinecraftServer.func_71263_m(MinecraftServer.java:110)
	at org.bukkit.craftbukkit.v1_5_R3.CraftServer.shutdown(CraftServer.java:1093)
	at org.bukkit.Bukkit.shutdown(Bukkit.java:394)
	at org.bukkit.command.defaults.StopCommand.execute(StopCommand.java:28)
	at org.bukkit.command.SimpleCommandMap.dispatch(SimpleCommandMap.java:189)
	at org.bukkit.craftbukkit.v1_5_R3.CraftServer.dispatchCommand(CraftServer.java:561)
	at org.bukkit.craftbukkit.v1_5_R3.CraftServer.dispatchServerCommand(CraftServer.java:544)
	at net.minecraft.server.dedicated.DedicatedServer.func_71333_ah(DedicatedServer.java:364)
	at net.minecraft.server.dedicated.DedicatedServer.func_71190_q(DedicatedServer.java:321)
	at net.minecraft.server.MinecraftServer.func_71217_p(MinecraftServer.java:303)
	at net.minecraft.server.MinecraftServer.run(MinecraftServer.java:195)
	at net.minecraft.server.ThreadMinecraftServer.run(SourceFile:573)
2013-07-07 16:12:13 [INFO] [TickThreading] Saving all player data.
2013-07-07 16:12:13 [INFO] [TickThreading] Done saving player data, now saving 2 worlds.
2013-07-07 16:12:13 [INFO] [TickThreading] World save completed, flushing world data to disk.
2013-07-07 16:12:13 [INFO] [TickThreading] Flushed world data to disk.
2013-07-07 16:12:13 [INFO] [TickThreading] Stopping the server. serverRunning: false, serverIsRunning: true, is crash: false