The CPU QB will definitely run. I've seen Tom Brady run against my team 3 times in one game. The problem is your QB. There is a discussion in the Coach Mode thread about this.
http://www.operationsports.com/forum...e-16-a-35.html
It was suppossedly happening before the patch and tuner though not very often.
Some people have tried the two controller method where you move both controllers to your team and set player lock on the guest controller to a lineman. Then set player lock on the main controller to another position, usually another lineman, to see if your QB would run. People that have tried this including myself have not seen the QB run.