You may have a scheduled task you are unaware of becasue something you added, removed, or changed scheduled something.
To see them, click Start then All Programs then Accessories then System Tools then Scheduled Tasks and see what is there. I found after removing Uniblue SpeedUpMyPC which I tested for a friend, it did a pretty good job removing itself compared to some I have seen, it cleaned out its registry stuff as well as its exe and dll's but it left a task in the Task Scheduler that was set to fire every hour for some reason. I deleted the task and the problem was gone.
If not there, it gets harder to track down, next I might try the Event Viewer and see if any critical system events are in the logs, if there are they may well lead you to the culprit. Make sure to write down the time it happens and then you can use the event views to look though the various logs for an event at that time.
Event Viewer access -- Control Panel / Administrative Tools / Computer Management / Event Viewer -- Then look through the various logs you will see listed for an event at that time, if you are lucky there will be one and that will be the guilty party.
You can also bring up the Task Manager (Ctrl-Alt-Del / Task Manager, then click the CPU heading to sort max CPU usage to the top of the list, then set and wait, chances are that it will eat some CPU just long enough for you to see who was trying something when you got the stop noise (this is by far the hardest and least reliable way to find it as stuff is happening all the time and so it would be easy by something to jump up that is totally unrelated.
Finally, well at least for me, you can get the MS Power Tools, specifically the Process Explorer and Process Monitor, these are like the task manager on steroids, and give the ability to log, so you could turn on logging while monitoring, wait for the event, then stop the logging and go look.
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