On the contrary, these are pauses with the hard disk light off. They also occur at times when no writes are (or at last should) be happening, and I had precisely zero disk performance troubles with the same drive under Linux..
Are you sure you have not been rooted then?
I have always hated MS Windows. From Windows 3.11 to Windows 7 I have always noted the big pauses caused by writes to the hard drive, problems that never showed up on my Amigas, Beos or Haiku machines.
Windows in particular is always writing back data to the hard drive, then acting like it never buffered the data, resulting in the system pausing at random.
However, once I added a SSD to my netbook, as far as I can detect all that pausing went away. Note: I am using Window 7 Starter, maybe you have a lot more services running in the background to slow you down, but beware being rooted!