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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 a new jenkins.war in place. Otherwise we can get these same symptoms (disappearing nodes) and see this same error with a 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 further testing we can get this same error to occur with different versions of Jenkins. For an existing installation we are seeing this same issue when we update to Jenkins 1.562 ("incompatible InnerClasses attribute between "hudson.model.Queue$ItemList" and "hudson.model.Queue"). Whereas dropping in-place a lower Jenkins version such as 1.528 does not show this issue.