[00:12:56] [Server thread/WARN]: java.net.ConnectException: Connection timed out: connect
[00:12:56] [Server thread/WARN]:         at java.net.TwoStacksPlainSocketImpl.socketConnect(Native Method)
[00:12:56] [Server thread/WARN]:         at java.net.AbstractPlainSocketImpl.doConnect(Unknown Source)
[00:12:56] [Server thread/WARN]:         at java.net.AbstractPlainSocketImpl.connectToAddress(Unknown Source)
[00:12:56] [Server thread/WARN]:         at java.net.AbstractPlainSocketImpl.connect(Unknown Source)
[00:12:56] [Server thread/WARN]:         at java.net.PlainSocketImpl.connect(Unknown Source)
[00:12:56] [Server thread/WARN]:         at java.net.SocksSocketImpl.connect(Unknown Source)
[00:12:56] [Server thread/WARN]:         at java.net.Socket.connect(Unknown Source)
[00:12:56] [Server thread/WARN]:         at sun.security.ssl.SSLSocketImpl.connect(Unknown Source)
[00:12:56] [Server thread/WARN]:         at sun.security.ssl.BaseSSLSocketImpl.connect(Unknown Source)
[00:12:56] [Server thread/WARN]:         at sun.net.NetworkClient.doConnect(Unknown Source)
[00:12:56] [Server thread/WARN]:         at sun.net.www.http.HttpClient.openServer(Unknown Source)
[00:12:56] [Server thread/WARN]:         at sun.net.www.http.HttpClient.openServer(Unknown Source)
[00:12:56] [Server thread/WARN]:         at sun.net.www.protocol.https.HttpsClient.<init>(Unknown Source)
[00:12:56] [Server thread/WARN]:         at sun.net.www.protocol.https.HttpsClient.New(Unknown Source)
[00:12:56] [Server thread/WARN]:         at sun.net.www.protocol.https.AbstractDeleg ... on.getNewHttpClient(Unknown Source)
[00:12:56] [Server thread/WARN]:         at sun.net.www.protocol.http.HttpURLConnection.plainConnect0(Unknown Source)
[00:12:56] [Server thread/WARN]:         at sun.net.www.protocol.http.HttpURLConnection$6.run(Unknown Source)
[00:12:56] [Server thread/WARN]:         at sun.net.www.protocol.http.HttpURLConnection$6.run(Unknown Source)
[00:12:56] [Server thread/WARN]:         at java.security.AccessController.doPrivileged(Native Method)
[00:12:56] [Server thread/WARN]:         at java.security.AccessController.doPrivilegedWithCombiner(Unknown Source)
[00:12:56] [Server thread/WARN]:         at sun.net.www.protocol.http.HttpURLConnection.plainConnect(Unknown Source)
[00:12:56] [Server thread/WARN]:         at sun.net.www.protocol.https.AbstractDelegateHttpsURLConnection.connect(Unknown Source)
[00:12:56] [Server thread/WARN]:         at sun.net.www.protocol.http.HttpURLConnection.getInputStream0(Unknown Source)
[00:12:56] [Server thread/WARN]:         at sun.net.www.protocol.http.HttpURLConnection.access$200(Unknown Source)
[00:12:56] [Server thread/WARN]:         at sun.net.www.protocol.http.HttpURLConnection$9.run(Unknown Source)
[00:12:56] [Server thread/WARN]:         at sun.net.www.protocol.http.HttpURLConnection$9.run(Unknown Source)
[00:12:56] [Server thread/WARN]:         at java.security.AccessController.doPrivileged(Native Method)
[00:12:56] [Server thread/WARN]:         at java.security.AccessController.doPrivilegedWithCombiner(Unknown Source)
[00:12:56] [Server thread/WARN]:         at sun.net.www.protocol.http.HttpURLConnection.getInputStream(Unknown Source)
[00:12:56] [Server thread/WARN]:         at sun.net.www.protocol.https.HttpsURLConnectionImpl.getInputStream(Unknown Source)
[00:12:56] [Server thread/WARN]:         at java.net.URL.openStream(Unknown Source)
[00:12:56] [Server thread/WARN]:         at ruby.bamboo.UpdateNotify.run(UpdateNotify.java:43)
[00:12:56] [Server thread/WARN]:         at java.lang.Thread.run(Unknown Source)
[00:12:56] [Server thread/WARN]:         at ruby.bamboo.BambooCore.preLoad(BambooCore.java:59)
[00:12:56] [Server thread/WARN]:         at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
[00:12:56] [Server thread/WARN]:         at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
[00:12:56] [Server thread/WARN]:         at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
[00:12:56] [Server thread/WARN]:         at java.lang.reflect.Method.invoke(Unknown Source)
[00:12:56] [Server thread/WARN]:         at cpw.mods.fml.common.FMLModContainer.handleModStateEvent(FMLModContainer.java:532)
[00:12:56] [Server thread/WARN]:         at sun.reflect.GeneratedMethodAccessor3.invoke(Unknown Source)
[00:12:56] [Server thread/WARN]:         at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
[00:12:56] [Server thread/WARN]:         at java.lang.reflect.Method.invoke(Unknown Source)
[00:12:56] [Server thread/WARN]:         at com.google.common.eventbus.EventSubscriber.handleEvent(EventSubscriber.java:74)
[00:12:56] [Server thread/WARN]:         at com.google.common.eventbus.SynchronizedEventSubscriber.handleEvent(SynchronizedEventSubscriber.java:47)
[00:12:56] [Server thread/WARN]:         at com.google.common.eventbus.EventBus.dispatch(EventBus.java:322)
[00:12:56] [Server thread/WARN]:         at com.google.common.eventbus.EventBus.dispatchQueuedEvents(EventBus.java:304)
[00:12:56] [Server thread/WARN]:         at com.google.common.eventbus.EventBus.post(EventBus.java:275)
[00:12:56] [Server thread/WARN]:         at cpw.mods.fml.common.LoadController.sendEventToModContainer(LoadController.java:212)
[00:12:56] [Server thread/WARN]:         at cpw.mods.fml.common.LoadController.propogateStateMessage(LoadController.java:190)
[00:12:56] [Server thread/WARN]:         at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
[00:12:56] [Server thread/WARN]:         at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
[00:12:56] [Server thread/WARN]:         at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
[00:12:56] [Server thread/WARN]:         at java.lang.reflect.Method.invoke(Unknown Source)
[00:12:56] [Server thread/WARN]:         at com.google.common.eventbus.EventSubscriber.handleEvent(EventSubscriber.java:74)
[00:12:56] [Server thread/WARN]:         at com.google.common.eventbus.SynchronizedEventSubscriber.handleEvent(SynchronizedEventSubscriber.java:47)
[00:12:56] [Server thread/WARN]:         at com.google.common.eventbus.EventBus.dispatch(EventBus.java:322)
[00:12:56] [Server thread/WARN]:         at com.google.common.eventbus.EventBus.dispatchQueuedEvents(EventBus.java:304)
[00:12:56] [Server thread/WARN]:         at com.google.common.eventbus.EventBus.post(EventBus.java:275)
[00:12:56] [Server thread/WARN]:         at cpw.mods.fml.common.LoadController.distributeStateMessage(LoadController.java:119)
[00:12:56] [Server thread/WARN]:         at cpw.mods.fml.common.Loader.preinitializeMods(Loader.java:556)
[00:12:56] [Server thread/WARN]:         at cpw.mods.fml.server.FMLServerHandler.beginServerLoading(FMLServerHandler.java:88)
[00:12:56] [Server thread/WARN]:         at cpw.mods.fml.common.FMLCommonHandler.onServerStart(FMLCommonHandler.java:320)
[00:12:56] [Server thread/WARN]:         at net.minecraft.server.dedicated.DedicatedServer.func_71197_b(DedicatedServer.java:176)
[00:12:56] [Server thread/WARN]:         at net.minecraft.server.MinecraftServer.run(MinecraftServer.java:631)
[00:12:56] [Server thread/WARN]:         at java.lang.Thread.run(Unknown Source)

应该是某个插件或者MOD的自动更新开启了但是却不能连接到它更新要用的网站
java.net.ConnectException
这个一般是指Socket没创建，如果楼主的电脑网络没有问题的话那就是更新的服务器坏了。
不过这个报错信息应该不影响楼主的服务端正常运行