The performance counters have likely been disabled, either unintentionally or by the OS for faulting too many times. Try using the exctrlst.exe tool to reenable them, reboot, then try using SiteScope again.
http://blogs.technet.com/b/yongrhee/archive/2009/10/06/how-to-rebuild-performance-counters-on-windows-vista-server2008-7-server2008r2.aspx
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