I've discovered something: this only happens after I've gamed with my Nvidia card, not the 'onboard' one. I can logout to get rid of the pause, or reboot.
This is so strange. It may happen a couple of times a day, or not at all. When it does happen there will be, every minute or 30 seconds, a 2-second delay to both typing and scrolling. This affects three browsers, Steam and Windows itself. I can get rid of it by rebooting, but not much else...