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This is still a problem as of version 1.574
Attempted automatic upgrade from 1.574 to 1.582 and screen stuck on "Jenkins restarting ..." Stop the Jenkins service and copy "jenkins.war.tmp" to "jenkins.war" and restart service. Upgrade is now complete.
Appears as if upgrade is waiting for the downloaded temporary war to replace the currently active war and this is hanging. My Jenkins is installed in the default "C:\Program Files (x86)\Jenkins\" directory so I would expect that the update process would need elevated privileges, though I suspect it already has them since it can place the new downloaded war file in that directory.
Hope that helps.