Just to play devil's advocate, I recently had a situation where my studio computer picked up a nasty bug that somehow got around the virus protection.
It required me to run registry sweeps and other malware removers to clean it up, but I got it back up and running quickly. Except that on the next boot, I got a nag screen (with a countdown locking the computer for a few seconds) from the tyrants of Redmond saying my computer no longer passed Microsoft Genuine Advantage tests.
I've owned this computer for years, qualified for regular MS updates, and never had a problem until now. I tried entering the reg key from the label on the case manually, I tried editing registry scripts, the auto phone authorization, nothing worked. Microsoft adamantly declared I was using unauthorized software, locked me out of the update website, hassled me with nag screens at startup, regular taskbar popups, a constant admonition that my computer may be at risk on the desktop and they blacked out the desktop background image. The only solution, according to these screens, was to update to a genuine Windows 7 license at $149.
It finally took a call to Microsoft Tech Support to point me to a tool that rescans the registry and resets the computer to pass the Genuine Advantage tests. (Thank you to the outsourced MS techie, a fellow with a heavy Indian accent who insisted his name was "Homer.")
A lot of trouble and "guilty until proven innocent" for someone with a legitimate license, don't you think?