This is what happened when the ScoreboardTimer reached zero and should have stopped the server
31.08 01:25:32 [Server] WARNING No compatible nms block class found.
31.08 01:25:30 [Server] SEVERE at java.util.TimerThread.run(Timer.java:505)
31.08 01:25:30 [Server] SEVERE at java.util.TimerThread.mainLoop(Timer.java:555)
31.08 01:25:30 [Server] SEVERE at main.TimerTest$1.run(TimerTest.java:117)
31.08 01:25:30 [Server] SEVERE at main.TimerTest.action(TimerTest.java:169)
31.08 01:25:30 [Server] SEVERE java.lang.NullPointerException
31.08 01:25:30 [Server] SEVERE Exception in thread "Timer-0" 
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This is what happened when the server first started up
31.08 01:24:58 [Server] INFO at net.minecraft.server.v1_6_R2.ThreadServerApplication.run(SourceFile:582)
31.08 01:24:58 [Server] INFO at net.minecraft.server.v1_6_R2.MinecraftServer.run(MinecraftServer.java:391)
31.08 01:24:58 [Server] INFO at net.minecraft.server.v1_6_R2.DedicatedServer.init(DedicatedServer.java:151)
31.08 01:24:58 [Server] INFO at net.minecraft.server.v1_6_R2.MinecraftServer.a(MinecraftServer.java:250)
31.08 01:24:58 [Server] INFO at net.minecraft.server.v1_6_R2.MinecraftServer.f(MinecraftServer.java:290)
31.08 01:24:58 [Server] INFO at net.minecraft.server.v1_6_R2.MinecraftServer.l(MinecraftServer.java:313)
31.08 01:24:58 [Server] INFO at org.bukkit.craftbukkit.v1_6_R2.CraftServer.enablePlugins(CraftServer.java:264)
31.08 01:24:58 [Server] INFO at org.bukkit.craftbukkit.v1_6_R2.CraftServer.loadPlugin(CraftServer.java:282)
31.08 01:24:58 [Server] INFO at org.bukkit.plugin.SimplePluginManager.enablePlugin(SimplePluginManager.java:381)
31.08 01:24:58 [Server] INFO at org.bukkit.plugin.java.JavaPluginLoader.enablePlugin(JavaPluginLoader.java:457)
31.08 01:24:58 [Server] INFO at org.bukkit.plugin.java.JavaPlugin.setEnabled(JavaPlugin.java:217)
31.08 01:24:58 [Server] INFO at main.TimerTest.onEnable(TimerTest.java:108)
31.08 01:24:58 [Server] INFO at main.TimerTest.doTimer(TimerTest.java:441)
31.08 01:24:58 [Server] INFO java.lang.NullPointerException
31.08 01:24:58 [Server] SEVERE Error occurred while enabling ScoreboardTimer v0.6 (Is it up to date?)
31.08 01:24:58 [Server] INFO ScoreboardTimer V0.6 enabled!