Not sure if you have already solved this, I had this issue on the CESM Server sometime back too, actually both cmdagent and antivirus takes turn to hog system resources. rebooting, Uninstalling and reinstalling doesnt help. So i contacted comodo support for this.
I cannot remember the root cause described by support, i remember it is due to a large log file created and then being 'scanned' but as the log file is appended all the time, cmdagent keeps scanning. Not sure what they did but after a few remote sessions with comodo support it was fixed.