We’ve encountered this too. The following usually helps, although it’s not a preventative measure, only a corrective one:
* Temporarily stop the automatic updates service. (you should see CPU drop)
* Download http://go.microsoft.com/fwlink/?LinkId=43264
* Run WindowsUpdateAgent20-x86.exe /wuforce
* Rename C:\windows\software distribution to C:\windows\software distribution.old
* Rename C:\windows\windowsupdate.log to c:\windows\windowsupdate.log.old
* restart the automatic updates service.