When it comes to disk activity, you can pretty much ignore CPU usage. 2% CPU usage or even much less is plenty to keep the disk busy. 98% idle makes total sense, even if the disk is thrashing as you describe. For a CPU, “waiting” means “doing nothing,” which in Process Explorer is considered idle.

The CPU is much faster than the disk, which means it’s actually spending most of its time waiting for the disk to read or write data. It’s quite possible for your CPU to be doing “nothing” while your disk thrashes. Let’s start by clarifying the CPU-usage issue. We’ll look at using Process Monitor to see if we can determine just exactly who’s doing what to your machine. FileMon has been replaced by a significantly more powerful utility, Process Monitor. In the past, I’ve recommended a tool called FileMon to determine what’s been writing to your disk. Your assumption that CPU usage is telling you something is incorrect. One thing I can tell you is, it’s not outside of Windows.

Technet sysinternals process monitor