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For further reference: I had exactly the same issue when running jobs on a Windows XP x64 slave. I had to unset HUDSON_COOKIE, HUDSON_SERVER_COOKIE, JENKINS_COOKIE or JENKINS_SERVER_COOKIE (I unset all of them, didn't check which one actually does the trick – JENKINS_COOKIE did not appear to be set though). We are running version 1.559, and the slave starts through JNLP (because we need it to access the GUI).
I found the solution based on this StackOverflow question referencing a comment on the Spawning process from build wiki page.
Notice that Jenkins continues to say that the process leaked file descriptors but at least it does not kill my background process any more (HSQLDB).