The Guardian reports that “One in five computers labelled as counterfeit by [Windows Genuine Advantage] are running legitimate operating systems”. They also point out that Microsoft has yet to explain why/how this is happening, or even make a good case for running WGA:

[T]he number of legitimate Windows users who have had problems indicates that the program isn’t working. And that’s where the WGA fiasco descends into farce. For a while WGA was listed as a critical update and installed at once if you had automatic updating selected – its purpose is really to fight piracy, which means that it’s not about security at all. The program itself is described (in its end user licence agreement, or EULA, which barely anyone reads) as “pre-release” – that is, beta, or in Microsoft’s preferred adjective, “pilot”.

Actually, piracy is about security, it’s just not usually considered the most critical aspect of security from the user’s perspective.