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Is there a firewall and/or load balancer between your java application and the Endeca MDEX? If so, are they setup bi-directionally? Is your java application running on linux? If so, what is your ulimit set to? http://webtools.live2support.com/linux/ulimit.php. If set too low, you could be running into a limit of the number of open handles (file and/or sockets) that your system will allow.
Sorry nothing too specific here...