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Some background before I get into the node name update process that worked for me. I'm configuring a bunch of load balanced blades on CentOS 5.4 with non-ARPing loopback configured by adding an entry to the rc.local file and to get "ifconfig" reading that, I wasn't rebooting, but just running "/etc/rc.d/rc.local".
Anyway, I too was frustrated by "uname -n" not being settable. I had some blades that reported different values, including the IP in their node name. That's what I wanted. I even tried strace -o, but all that told me was that uname was getting called! But I also had a bunch that didn't, instead just reporting "localhost.localdomain" as their nodename, so I knew there was something different in the process, and nothing config file related as I followed the same setup for all. Like you, nothing worked to set it...until I executed a reboot, at which point nodename updated to the desired change.
So, the setting is there somewhere in the init chain, not sure where yet, but you can try a reboot and hopefully that'll do it for you too.