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The hidden CPU processing is known as interrupt processing or fast path processing. This processing is not detailed in the proc cpu display. It represents the CPU processing being used to forward packets in the most optimal manner the router supports.
Some additional information on show processes cpu, can be found here:
http://www.cisco.com/en/US/products/sw/iosswrel/ps1828/products_tech_note09186a00800a65d0.shtml
