I have seen one such 'slow down windows file operations' but not random, I tried to replicate it but was unable to. Have you changed any of the default file system shield settings ?
What OS are you using, plus some info on your system (CPU and RAM) ?
Do you have any other security based software installed (anti-spyware, firewall, etc.) running at boot ?
You could check msconfog and see what startup items there are and be very selective in what you allow to run on boot, basically OS functions and your security applications. Many program set themselves to run on boot (medial players are a typical example), when they aren't required immediately.
There is a possibility that the auto update may be running very early if you have a broadband connection that is available very early in the boot process ?