I'm playing Skryim through Mod Organizer, with a variety of mods installed (can list if necessary). The only things I have running in the background are Steam, the AMD Catalyst interface, and BitTorrent. The AMD thing is the newest change... but it isn't that new; I've been running it for months. But every now and then, when I'm in combat with a one-handed weapon, it's like the mouse is clicking something in the background and forcing the game to minimize, taking me back to the desktop.

This has only been happening for a couple days now, and so far as I know there were no configuration changes between the last time I ran it without issues and recently.

I found http://www.gamesas.com/topic/1350702-game-acts-like-alt-tab-has-been-used/ from 2012 describing a similar issue, but the blame apparently was laid upon a program called xfire... which I've never heard before, and don't have installed, so far as I know. Does anyone else know what could be causing this?

Disable BitTorrent, if it's active and (maybe) downloading in the background.

I shut down the AMD Gaming Evolved software, and now I'm not having the problem. I never had a problem with it before... but I don't really use it for anything (it just rode along while I was updating my drivers), so I think I'll just get rid of it.