Quick question: Do you use a third party software program to defragment? If so, which one?
Pagefile, also called swap file, is the section of memory that the computer uses as secondary to the RAM. This file can get fragmented sometimes if your computer had to increase your virtual memory if you ran out. This happened to me before.
The masterfile is a section that that is something like an abbreviated index of the files and folders on your system. As you add files and folders, the masterfile increases in size. Unfortunately, when you get rid of files and folders, the corresponding space on the masterfile is still there.
Both these can be defragmented with certain third party defragmenters if you want to go that route.