Well, just to update. It happened again tonight even with focus follows mouse off. Not as bad as before though. So, it doesn't necessarily appear to have anything to do with focus follows mouse.

It seemed to happen primarily during boss fights tonight (go figure). Might be lag, I don't know. My keypresses become totally unresponsive and spells are going off that I am not activating. Some of these spells are not bound to any key. Maybe it's my G15 screwing up, but even when I hit my "2" DPS key sometimes nothing happens as well. Anyway, incredibly annoying. I might try some hardware-based system to see if that changes anything. So, far it's only been in instances as well. Relogging seemed to help, but that could be a coincidence.