I am facing this same issue as well. I just added a comment to JENKINS-5055.

On Friday, March 4, 2016 at 3:45:37 AM UTC-8, [email protected] wrote:
>
> Hi all,
>
> We have a Jenkins instance running on Ubuntu that has several slaves in 
> different systems. One of them is a Windows 7 host, having jenkins slave 
> instance configured as a service.
>
> We have a problem that when that machine is rebooted, master Jenkins 
> doesn't realize it's gone. It looks to be just fine in the nodes view. 
> Then, when a build is issued that is supposed to use that slave it gets 
> stuck. If that is stopped, the next build fails immediately
>
>     Caused by: java.util.concurrent.TimeoutException: Ping started at 
> 1457016721684 hasn't completed by 1457016961684
>     ... 2 more
>     [EnvInject] - [ERROR] - SEVERE ERROR occurs: channel is already closed
>
> When the slave has started up and it tries to connect back to master, 
> connection is refused, and in the logs there is an error saying connection 
> with that name already exists:
>
>     Server didn't accept the handshake: xxx is already connected to this 
> master. Rejecting this connection.
>
> There is issue JENKINS-5055 (
> https://issues.jenkins-ci.org/browse/JENKINS-5055) which claims a fix was 
> committed allowing the same JNLP slave to reconnect without getting 
> rejected, apparently commit 
> https://github.com/jenkinsci/jenkins/commit/68ed742227891a3f716e4e479388c36876bb935a,
>  
> and according to changelog (https://jenkins-ci.org/changelog-old.html), 
> it was introduced in version 1.396 (2011/02/02). We are however using 
> version 1.639 and seeing this. Somebody else (
> http://comments.gmane.org/gmane.comp.java.jenkins.user/29769) seems to be 
> seeing it as well. By looking at current codebase (
> https://github.com/jenkinsci/jenkins), I see where the error is coming 
> from (
> https://github.com/jenkinsci/jenkins/blob/master/core/src/main/java/jenkins/slaves/JnlpSlaveAgentProtocol.java#L104),
>  
> but don't see the fix done in JENKINS-5055.
>
> Any ideas on resolving this?
>
> (Note: also posted to 
> http://serverfault.com/questions/761342/jenkins-doesnt-recognize-slave-being-down
> )
>

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