I am having a similar problem. My FPS doesn't change while the lag is happening. All of my actions happen about 5 seconds after I perform them and at like half the normal speed. Alt tabbing back and forth to the game about 10 times seems to fix it.
I have two 6950s in crossfire. First time this happened I couldn't solve it, and trying to uninstall the CAP and driver (12.1 and 11.12 CAP 2) would make me bluescreen. I reformatted windows. This time I'm using 11.11 and the CAP that goes with that version, and the issue persists. This doesn't happen in any other game, so I'm pretty sure it's BF3.