Could be background processes. Also how often does it happen and does it happen when you're online? If it's happening when you're online it might be lag, that problem happens when I'm playing on battlefield 3 online sometimes with laggy servers.
Yea go into Task Manager and check your processes and see whats using the most CPU usage. If it says... Explorer.exe restart your computer. I find that FX heavily does that, makes your OS architecture sort of reveal it self and just bog your system