This problem can be caused by programs starting up and the defrag. then starts again from the beginning. Shut down ALL PROGS. such as screensavers, Broadband modems etc. and you should have no problems.
You didn't say what operating system you use. If it is still W98, click control/Alt/Delete, and end task every running program apart from Systray and explorer, also disable screensaver. It should then go through. If you use XP I would go along with the suggestion to use diskeeper.