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Another option would be that SCM's processWorkspaceBeforeDeletion(...) breaks things. What SCMs (Subversion, Git, Mercurial, ...) are used on the affected jobs? Does it also affect jobs that don't use any SCM?
What workspace listeners are in use when this occurs? Run WorkspaceListener.all() in Manage Jenkins ยป Script Console and report the output.
Re Workspace Cleanup plugin, maybe this should be changed to report failure to delete in one of the tries at least to the system log:
https://github.com/jenkinsci/ws-cleanup-plugin/blob/267f3/src/main/java/hudson/plugins/ws_cleanup/PreBuildCleanup.java#L103