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Here's what's happening:
1. Restarting Jenkins (after plugin-update or by calling /restart) spawns a new process to execute "jenkins.exe restart" (i.e., restarting via the Windows Service wrapper). The Parent Process ID of this new process equals the Process ID that is running jenkins.war.
2. Jenkins.exe's "restart" command is a three-part process: A) stop the jenkins.war PID and all children PID; B) Wait for jenkins.war PID to stop; C) launch jenkins.war in a new process.
3. Since this execution of "jenkins.exe restart" is itself a child process of jenkins.war, the Jenkins service is killing it as part of 2A. This results in:
3A. Killing "jenkins.exe restart" (via SIGINT) causes that process to return w/ errorlevel=1. The WindowsServiceLifecycle restart method is checking the errorlevel from running "jenkins.exe restart" and seeing that it is not 0, and therefore throws an IOException. This is the error message seen in jenkins.err.log.
3B. Since the process running "jenkins.exe restart" gets killed as part of Step 2A, it does not get a change to complete the restart process, so Jenkins remains stopped.
Solution:
From looking at the WinSW project, this issue was expected. A "restart!" command (vs. the standard "restart") was added that launches a new process to handle restart. WindowsServiceLifecycle should use the new command.