Well... I have a hunch that it has something to do with python-apt package
specifically the newest BaseURI vs. BaseURI-architecture implementation

I changed the file /usr/share/python-apt/templates/Ubuntu.info and
modified the following section as listed below:

Suite: hardy-security
ParentSuite: hardy
RepositoryType: deb
BaseURI-amd64: http://security.ubuntu.com/ubuntu
MatchURI-amd64: archive.ubuntu.com/ubuntu|security.ubuntu.com
BaseURI-powerpc: http://ports.ubuntu.com/
MatchURI-powerpc: ports.ubuntu.com/ubuntu
Description: Important security updates

Basically, I changed BaseURI to BaseURI-amd64 (my Ubuntu architecture), now it 
works.
Looks like BaseURI-arch is working better than BaseURI :)

** Also affects: software-properties
   Importance: Undecided
       Status: New

** Also affects: python-apt (Ubuntu)
   Importance: Undecided
       Status: New

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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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