I was getting pretty much the same warning saying this...

Reading package lists... Done
W: Duplicate sources.list entry http://security.ubuntu.com 
hardy-security/restricted Packages 
(/var/lib/apt/lists/security.ubuntu.com_ubuntu_dists_hardy-security_restricted_binary-amd64_Packages)
W: Duplicate sources.list entry http://security.ubuntu.com hardy-security/main 
Packages 
(/var/lib/apt/lists/security.ubuntu.com_ubuntu_dists_hardy-security_main_binary-amd64_Packages)
W: You may want to run apt-get update to correct these problems

I was having the same issue on my work network.  I noticed the protocol
being used is http and we have a web proxy/caching device (Blue Coat) on
the network.  I added security.ubuntu.com to a bypass of my cache and
this fixed my issue.  I wonder if any other users having the issue might
be behind a web proxy/cache (maybe even squid).   Just tossing that out
there.

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Checking security repository in Updates adds deb line to Third-Party Software
https://bugs.launchpad.net/bugs/244093
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