If it happens during playing all of your games, it's your windows loosing focus, now it might be or it might not be a background application causing it, the only solutions i know to this problem is either reinstall your whole system like me (cause i'm lazy) or do a clean boot to try and see which program is causing it, here's how to do that: http://support.microsoft.com/kb/331796/en
Like I said, it only happens with ME3. No other games and applications in general have ever done this, including Mass Effect and Mass Effect 2.