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I've seen this on my dev instance. It went away when I deleted the JENKINS_HOME, unfortunately I doubt this is an option for you.
Maybe delete extracted plugins and war to force them to be recreated.
Note that if you're asking for help, rather than reporting an issue, the jenkinsci-users list or #jenkins on Freenode would be better due to a larger audience. For tips how to ask, see http://www.catb.org/esr/faqs/smart-questions.html or https://wiki.jenkins-ci.org/display/JENKINS/How+to+report+an+issue