msmpeng.exe causes CPU spikes that happen every 15 mins or so, and it has finally got to me. As far as I can remember, I started facing this after installing MS Security Essentials on my Windows 7 Ultimate PC. I use genuine Windows, update it when updates are available and do not have any other anti-virus installed (I clean installed Avira using Revo before installing security essentials)
I've also added more exclusions, disabled behavior monitoring, limited CPU usage during quick scan which happens only once a week.. nothing seems to work. Every while or so, the computer will freeze for a minute or so, and when I can access task manager, I see msmpeng.exe at the top and then coming down slowly.
The last resort obviously would be going back to avira or avast or whatever, I'd prefer to keep using Security Essentials.