We're experiencing a similar issue the stacktrace is different, but the symptoms are the same, aborted builds in the middle of job execution.

Problems started after an upgrade from 1.556 to 1.564. I Think this could be a blocker.

Console.out
FATAL: hudson.remoting.RequestAbortedException: java.io.IOException: A connection attempt failed because the connected party did not properly respond after a period of time, or established connection failed because connected host has failed to respond
hudson.remoting.RequestAbortedException: hudson.remoting.RequestAbortedException: java.io.IOException: A connection attempt failed because the connected party did not properly respond after a period of time, or established connection failed because connected host has failed to respond
	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:739)
	at hudson.remoting.RemoteInvocationHandler.invoke(RemoteInvocationHandler.java:168)
	at com.sun.proxy.$Proxy45.join(Unknown Source)
	at hudson.Launcher$RemoteLauncher$ProcImpl.join(Launcher.java:951)
	at hudson.tasks.CommandInterpreter.join(CommandInterpreter.java:137)
	at hudson.tasks.CommandInterpreter.perform(CommandInterpreter.java:97)
	at hudson.tasks.CommandInterpreter.perform(CommandInterpreter.java:66)
	at hudson.tasks.BuildStepMonitor$1.perform(BuildStepMonitor.java:20)
	at hudson.model.AbstractBuild$AbstractBuildExecution.perform(AbstractBuild.java:745)
	at hudson.model.Build$BuildExecution.build(Build.java:198)
	at hudson.model.Build$BuildExecution.doRun(Build.java:159)
	at hudson.model.AbstractBuild$AbstractBuildExecution.run(AbstractBuild.java:518)
	at hudson.model.Run.execute(Run.java:1706)
	at hudson.model.FreeStyleBuild.run(FreeStyleBuild.java:43)
	at hudson.model.ResourceController.execute(ResourceController.java:88)
	at hudson.model.Executor.run(Executor.java:231)
Caused by: hudson.remoting.RequestAbortedException: java.io.IOException: A connection attempt failed because the connected party did not properly respond after a period of time, or established connection failed because connected host has failed to respond
	at hudson.remoting.Request.abort(Request.java:299)
	at hudson.remoting.Channel.terminate(Channel.java:802)
	at hudson.remoting.SynchronousCommandTransport$ReaderThread.run(SynchronousCommandTransport.java:69)
Caused by: java.io.IOException: A connection attempt failed because the connected party did not properly respond after a period of time, or established connection failed because connected host has failed to respond
	at sun.nio.ch.SocketDispatcher.read0(Native Method)
	at sun.nio.ch.SocketDispatcher.read(Unknown Source)
	at sun.nio.ch.IOUtil.readIntoNativeBuffer(Unknown Source)
	at sun.nio.ch.IOUtil.read(Unknown Source)
	at sun.nio.ch.SocketChannelImpl.read(Unknown Source)
	at hudson.remoting.SocketChannelStream$1.read(SocketChannelStream.java:33)
	at sun.nio.ch.ChannelInputStream.read(Unknown Source)
	at sun.nio.ch.ChannelInputStream.read(Unknown Source)
	at sun.nio.ch.ChannelInputStream.read(Unknown Source)
	at java.io.InputStream.read(Unknown Source)
	at sun.nio.ch.ChannelInputStream.read(Unknown Source)
	at hudson.remoting.FlightRecorderInputStream.read(FlightRecorderInputStream.java:82)
	at java.io.ObjectInputStream$PeekInputStream.peek(Unknown Source)
	at java.io.ObjectInputStream$BlockDataInputStream.peek(Unknown Source)
	at java.io.ObjectInputStream$BlockDataInputStream.peekByte(Unknown Source)
	at java.io.ObjectInputStream.readObject0(Unknown Source)
	at java.io.ObjectInputStream.readObject(Unknown Source)
	at hudson.remoting.Command.readFrom(Command.java:92)
	at hudson.remoting.ClassicCommandTransport.read(ClassicCommandTransport.java:70)
	at hudson.remoting.SynchronousCommandTransport$ReaderThread.run(SynchronousCommandTransport.java:48)
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