I would suggest you don't update whilst running a game. I'm on dial-up so I have my auto update set to ask (Program Settings, Update (basic)), but the check still takes place but not the actual update.
Did you actually record the CPU usage and what processes were using most of it ?
You should also check the 'Check for full screen applications (e.g. games) before displaying popups in Program Settings, Troubleshooting. Whilst that probably won't stop it checking it won't display any pop-up possibly taking focus.