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Now I am at 1.565.3. Right after the upgrade, this error was still hitting us. Then I reconfigured all Windows slaves as JNLP nodes with the same revision of the client software (2.46). After this, the situation improved a lot. The number /usr/sbin/lsof | grep protocol | grep [jenkins-pid] | wc -l increased less fast than before. And the server is much more stable.
I have the impression that the Windows clients are the root cause of the error. Maybe I should reconfigure them simply as SSH slaves.