Basically, from what I understand, the file fragments that remain are part of "file sharing " betweeen programs. 
This is often the case with programs that  are related such as Gator, GoZilla,Front Page, Dreamweaver, Homesite... and allot of the Norton products that have the exact same code as a competitive product so when you install.....rather than overwriting they simply share a file.
When you defrag it is a tug of war as to where to move the file so it just stays in the same place...."fragmented" but not really....just caught in the middle. Just MY understanding of it.....( I could be full of Zhoot ?)
Anyone else ????