Pretty much. I've seen one system that would pause for about 20 seconds. Turned out to be a failing hard drive.
Sorry for all the questions. Trying to narrow this down a bit. Can you run CrystalDiskInfo to make sure the drive health is good on the Win7 side:
http://crystalmark.info/software/CrystalDiskInfo/index-e.html
Normally wondering about the HDD wouldn't come to mind with two OS running differently (drivers would) but since Windows and Linux place things different on the drive, hence no constant need for defrag on Linux, i wonder if some sectors on the drive are bad that Windows is on.