I _hate_ this notification of having to reboot my system for some update to start having it's effect. Furthermore, in most cases, I'm quite convinced it's just a precaution by the Microsoft team to ensure some patch didn't bork.
Anyways, to prevent this, just follow these easy steps...
1. Start -> Run -> gpedit.msc
3. Computer Configuration -> Administrative Templates -> Windows Components -> Windows Update
4. Enable "No auto-restart for scheduled Automatic Update installations"
5. Disable "Re-prompt for restart with schedule installations"
You'll have to restart your computer after this before it starts working... ;) (no, really)
Of course, you could always just drag the notification window to your uber bottom left corner and let it sit there eternally :)
Hope it helps ya