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Happens to me with a freestyle project with 1.598, Windows master, Linux slave (debian wheezy).
When I abort a job, it appears as aborted in Jenkins, but keeps running.
The following exception appears in the log.
Project #362 aborted java.lang.InterruptedException at java.lang.Object.wait(Native Method) at hudson.remoting.Request.call(Request.java:146) at hudson.remoting.Channel.call(Channel.java:751) at hudson.remoting.RemoteInvocationHandler.invoke(RemoteInvocationHandler.java:179) at com.sun.proxy.$Proxy47.isAlive(Unknown Source) at hudson.Launcher$RemoteLauncher$ProcImpl.isAlive(Launcher.java:984) at hudson.plugins.xshell.XShellBuilder.perform(XShellBuilder.java:140) at hudson.tasks.BuildStepMonitor$1.perform(BuildStepMonitor.java:20) at hudson.model.AbstractBuild$AbstractBuildExecution.perform(AbstractBuild.java:761) at hudson.model.Build$BuildExecution.build(Build.java:199) at hudson.model.Build$BuildExecution.doRun(Build.java:160) at hudson.model.AbstractBuild$AbstractBuildExecution.run(AbstractBuild.java:536) at hudson.model.Run.execute(Run.java:1718) at hudson.model.FreeStyleBuild.run(FreeStyleBuild.java:43) at hudson.model.ResourceController.execute(ResourceController.java:89) at hudson.model.Executor.run(Executor.java:240)