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In my experience this issue occurs whenever Jenkins restarts, shuts down, or crashes while builds are running: The folder is created to hold the build log etc., but the build.xml file describing the build is (usually) only created once a build is finished. So any of these folders are likely the result of a sudden shutdown of Jenkins and their status as warning appropriate.
The simple workaround is to throw away these incomplete folders Jenkins complains about until there are no more warnings left.
Maybe the out-of-order build monitor could be extended to allow cleanup of incomplete build dirs.