Hi Katamoran, Welcome to THW.
This is kind of a shot in the dark, but it may be windows indexing service trying to work in the background. Or I believe Win7 also has a feature that will use idle CPU time to defrag your PC, but but I wouldn't think that it would cause such off CPU usage or happen as soon as your CPU goes idle. There is another windows feature that i cannot recall what it is that may also cause this behavior.
Have you looked into your task manager while this is happening, without ANY programs opened and checked for programs using alot of your system resources or that seem to be out of place?