I've seen this on several occasions under Windows, and it's enough to drive one bat-shit mad. I'll be happily tooling away when out of nowhere, a software update will impose itself on whatever I'm doing. Great, thanks! Worse is the default behavior of programs like Lotus Notes, which ship by default to put up a notification window that "YOU'VE GOT MAIL!" which not only brings Lotus Notes to the foreground, but makes it impossible to continue without dismissing the notification. I'm surprised nobody has taken the time to eradicate this from the default loads, because it's a real focus destroying move.
And, just to put my usual Linux spin on this, GNOME and Ubuntu thankfully keep your focus, and pop up underneath whatever window you're currently in, while flashing the in the task list. It's very handy. Oh, and software updates are notified in the notification area. Even better, you can remove the notification area if you so choose.