If you are running the 6.7 agent, you can safely delete the \jre6.3.1.hotfix directory. This directory is not used by the latest agent and is likely there as a result of an auto-upgrade, but no longer used. The 6.7 agent leverages OpenJDK and does not require Oracle Java. Can you remove the directory, re-run the Nessus scan and confirm that you no longer see the vulnerability?
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