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UserFriendly - 2:20 am on Jan 31, 2010 (gmt 0)
Usually when a site gets taken over like that, it's through unpatched blogging software such as Wordpress, etc, so if you are using any pre-packaged software tools on your site, check that they're the latest version.
Have you positively linked the trojan is linked to site hijacking? (Not something I've heard of before.) A lot of Windows machines are infected with malware, and it may be a coincidence.