Love this game. Been playing it for about a year. Since the 4.0.1 release, I've periodically run into issues with it freezing for several seconds at a time. During these moments of freezing the CPU is pegged.
It's been driving me crazy, but I finally tracked it down. It appears to be the bone crusher AI. A good way to test this is to set up a skirmish with several bone crusher AI opponents. After a couple of minutes the issue starts and it'll hang. Presumably if you have a fast enough CPU, maybe it would just spike the CPU at those times. I have a Phenom X6 running 2.9 GHz, so not a top of the line gaming box, but it's never had issues with any of the other AIs.