This program is almost completely I/O bound. It spends all its time sleeping so its CPU usage is nearly zero. There might be some disk contention from other programs, but I would think that should be fairly constant. I am re-testing with longer run times to check this.
You give up your time slice to the operating system when you block waiting on I/O. If the operating system doesn't return control to you before your current I/O completes then you'll certainly slow down. I've seen current versions of windows just freeze for long periods if a CD isn't readable, so I'm certain this can happen. Given Ivan's notes about how NTFS works under the covers I would bet on his idea over mine though.
