Seems that Brad Baker over at Joomla had an interesting time with an organization that didn't even know that they were using Joomla!. Read about it here. The media and security companies have people worried so much about hackers and viruses that they don't just take a step back and take everything in. I guess its "better to be safe than sorry". But it would atleast help if they talked to their webmasters and/or their system admins before assuming their site has been hacked. For all they know it could just be system admin tightening up security so much that the web server doesn't let anyone in, even if they are just viewing a webpage.
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