Most OSes have some code that runs when other processes aren't running to measure the idle time. Certainly in Windows, this is a process in it's own right.
If the CPU is only 1% utilised, then the idle time process is consuming most of the remaining 99% (with the kernel using a bit of that).
So, I would hazard a guess that it's something in this.
(Or, for Windows, the code that swaps pages out to disk.)