You might want to try using sysinternals process explorer and see what spikes your cpu usage.
I had a incident a few days ago where a scanner was operating jerky, and stalling out the box. I saw under process manager where "system" was maxing out the cpu when it stuttered, so I ran the above mentioned tool and watched. Lo and behold, it was the telephony windows service causing the stutter.
I disabled the service and the machine started running fine. I have no idea what telephony has to do with scanning.
