Using the most recent build of Jenkins I have been seeing connection issues after issuing reboot commands to targets. After looking at some logs it looks like the slave service on Windows may not be shutting down correctly and is not disconnecting from the Jenkins Server. I suspect that this is causing the reconnect issues that I'm seeing after the machine comes back online. Below is the failure as reported by the Jenkins server and excerpts from log files on the slave machine when the issue reproduced.

Error as reported from Jenkins Server:
FATAL: hudson.remoting.RequestAbortedException: java.net.SocketException: Connection reset
hudson.remoting.RequestAbortedException: hudson.remoting.RequestAbortedException: java.net.SocketException: Connection reset
at hudson.remoting.RequestAbortedException.wrapForRethrow(RequestAbortedException.java:41)
at hudson.remoting.RequestAbortedException.wrapForRethrow(RequestAbortedException.java:34)
at hudson.remoting.Request.call(Request.java:174)
at hudson.remoting.Channel.call(Channel.java:722)
at hudson.FilePath.act(FilePath.java:1009)
at org.jenkinsci.plugins.envinject.service.EnvironmentVariablesNodeLoader.gatherEnvironmentVariablesNode(EnvironmentVariablesNodeLoader.java:44)
at org.jenkinsci.plugins.envinject.EnvInjectListener.loadEnvironmentVariablesNode(EnvInjectListener.java:81)
at org.jenkinsci.plugins.envinject.EnvInjectListener.setUpEnvironment(EnvInjectListener.java:39)
at hudson.model.AbstractBuild$AbstractBuildExecution.createLauncher(AbstractBuild.java:575)
at hudson.model.AbstractBuild$AbstractBuildExecution.run(AbstractBuild.java:481)
at hudson.model.Run.execute(Run.java:1700)
at hudson.model.FreeStyleBuild.run(FreeStyleBuild.java:43)
at hudson.model.ResourceController.execute(ResourceController.java:88)
at hudson.model.Executor.run(Executor.java:231)
Caused by: hudson.remoting.RequestAbortedException: java.net.SocketException: Connection reset
at hudson.remoting.Request.abort(Request.java:299)
at hudson.remoting.Channel.terminate(Channel.java:782)
at hudson.remoting.SynchronousCommandTransport$ReaderThread.run(SynchronousCommandTransport.java:69)
Caused by: java.net.SocketException: Connection reset
at java.net.SocketInputStream.read(SocketInputStream.java:185)
at java.io.FilterInputStream.read(FilterInputStream.java:133)
at java.io.BufferedInputStream.fill(BufferedInputStream.java:235)
at java.io.BufferedInputStream.read(BufferedInputStream.java:254)
at hudson.remoting.FlightRecorderInputStream.read(FlightRecorderInputStream.java:77)
at java.io.ObjectInputStream$PeekInputStream.peek(ObjectInputStream.java:2265)
at java.io.ObjectInputStream$BlockDataInputStream.peek(ObjectInputStream.java:2558)
at java.io.ObjectInputStream$BlockDataInputStream.peekByte(ObjectInputStream.java:2568)
at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1314)
at java.io.ObjectInputStream.readObject(ObjectInputStream.java:368)
at hudson.remoting.Command.readFrom(Command.java:92)
at hudson.remoting.ClassicCommandTransport.read(ClassicCommandTransport.java:71)
at hudson.remoting.SynchronousCommandTransport$ReaderThread.run(SynchronousCommandTransport.java:48)

From jenkins-slave.err.log:

Apr 19, 2014 11:52:09 PM hudson.remoting.jnlp.Main createEngine
INFO: Setting up slave: <Slave Machine>
Apr 19, 2014 11:52:09 PM hudson.remoting.jnlp.Main$CuiListener <init>
INFO: Jenkins agent is running in headless mode.
Apr 19, 2014 11:52:09 PM hudson.remoting.jnlp.Main$CuiListener status
INFO: Locating server among http://<Jenkins Server>/
Apr 19, 2014 11:52:09 PM hudson.remoting.jnlp.Main$CuiListener status
INFO: Connecting to <Jenkins Server>
Apr 19, 2014 11:52:09 PM hudson.remoting.jnlp.Main$CuiListener status
INFO: Handshaking
Apr 19, 2014 11:52:09 PM hudson.remoting.jnlp.Main$CuiListener error
SEVERE: The server rejected the connection: <Slave Machine> is already connected to this master. Rejecting this connection.
java.lang.Exception: The server rejected the connection: <Slave Machine> is already connected to this master. Rejecting this connection.
at hudson.remoting.Engine.onConnectionRejected(Engine.java:303)
at hudson.remoting.Engine.run(Engine.java:276)

From jenkins-slave.wrapper.log:

2014-04-19 23:52:14 - Stopping jenkinsslave-C__Jenkins
2014-04-19 23:52:14 - ProcessKill 3088
2014-04-19 23:52:15 - Shutdown exception
Message:A system shutdown is in progress. (Exception from HRESULT: 0x8007045B)
Stacktrace: at System.Runtime.InteropServices.Marshal.ThrowExceptionForHRInternal(Int32 errorCode, IntPtr errorInfo)
at System.Management.ManagementScope.InitializeGuts(Object o)
at System.Management.ManagementScope.Initialize()
at System.Management.ManagementObjectSearcher.Initialize()
at System.Management.ManagementObjectSearcher.Get()
at winsw.WrapperService.StopProcessAndChildren(Int32 pid)
at winsw.WrapperService.StopIt()
at winsw.WrapperService.OnShutdown()