Hello,
have you checked the execution stack when CPU usage was high? Looking at a dump of the thread stacks at that time tells you what might be running wild. Since it is every two hours flat, I'd assume you have a scheduled job running in Alfresco, a client that is calling an intensive operation in Alfresco or on the operating system. What does your OS process list tell you in regards to which process is actually using up the CPU?
Regards
Axel