I came here to post almost this exact same thing. With mine, it pops up when I minimize the game (also BF3) to do something else, and completely ignores the checkbox telling it not to do it again. Sometimes it doesn't even ask - I just get a message telling me it's changed my theme to basic, and for some reason I can't reactivate aero themes without restarting my computer.
The stupidest part is that even with the game running, the computer doesn't actually go slowly. It has plenty of memory and doesn't bother the cpu much at all, and I often have it do multiple other things while playing. This feature just seems to be bugged.