That means that its not System Idle Process that has 99% of the CPU as this doesn't show up under the performance tab as its actually not a process that are using any CPU power.
Go into your task manager go to the process tab now click on the CPU column it will now sort it in processes using CPU (you probably need to press it twice to list the highest process at the top) now check what process(es) have the highest number after it.
Common processes that use a lot of cpu is antivirus if its busy scanning files, if you use EPO to update your McAffee antivirus it is very prone to go bust and sit and user 99% cpu.
Also viruses, spyware etc is common types of "software" using a lot of process power.
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Make the best use of what is in your power, and take the rest as it happens.
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