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Was this an in-place update/upgrade that done recently from a previous version of Jenkins (or even hudson)? At least on RHEL with tomcat we have had to remove the old directory under webapps when dropping the new jenkins.war in place. Otherwise we can get these same symptoms (disappearing nodes) and see this same error with slightly different stack trace immediately after a fresh in-place upgrade.
Also note there is a ~/.jenkins/cache directory where jar file versions may be. Don't suggest you play in there unless step above has been tried and then, if still failing, after you have stopped jenkins to rename/delete cache contents.
With additional testing with in-place .war update Jenkins 1.528 does not show this issue ("incompatible InnerClasses attribute between "hudson.model.Queue$ItemList" and "hudson.model.Queue"). Whereas as dropping in-place higher Jenkins versions including 1.562 does have this issue.