I want/need to keep some version of Windows around for many games, but I was trying to repartition my disk so I could add a couple more partitions for Linux and perhaps BSD. The software I was using didn't want to work on a disk with an error (probably quite correctly), thus the need for chkdsk.
While I was doing this, I also ran defragmentation (hey, wait a minute, I thought NTFS would never need defragmentation and it was so shiny-perfect it would never need chkdsk and ....)