You've almost certainly got something running in the background ... do what the 2 other posters said, stop background activities, or run it in safe mode
If you are using Win98 or WinME, find a freeware version of a program called Power defrag. This stops all activities, reboots and does the defrag for you. On completion the program will reboot your computer.
You don't mention what OS you are using or what Defrag program.Obtain a copy of Diskeeper (latest version is 10). you do not have to turn off programs etc.