See also 27864.
We have experienced deadlock problems with restarting jenkins.
Investigation learned that they seem to be caused by the sonar plugin version 2.2 and 2.2.1. We found what we think is the culprit by looking at a lot of the deadlock reports.
Different plugins were seen in those reports, but 1 was always there:
◾locked <0x00000000e1044ca8> (a hudson.plugins.sonar.SonarPublisher$DescriptorImpl)
Reverting back to plugin version 2.1 resolved the problem.