I have had similiar problems in the past with some software. Various manufacturers provide drivers for printers (eg HP, Dell etc) The same is true for some other peripheral devices. These drivers (any particularly early ones) forgot to let go of the processor when they had finished their slot. hence the processor went round in circles for a while waiting ....
Try removing (or even uninstalling peripheral devices like printers cameras etc and see if that helps. It certainly seems as though a ,process is hogging the CPU but have a look in the list of processes running in the task manager (as you have done) and look at those that have a high CPU usage. You can then turn them off so that they do not start unless manually started but as you are aware do not turn off the critic windows ones (but be aware that some critical windows processes are started by a different thread (eg USB devices!)
M
