I have 98SE and I restart my system in "Safe Mode". In this mode it is running with the minimum of system resources. This means nothing to interfere with the defrag operation.
If you do not know how to get into "Safe Mode" post back and we will walk you through the procedure.
DC
every time i try to use disc defragmenter it seems to keep going back to the beginning after notifying me that the disc's contents have changed. I have closed all other programmes and have set the screensaver to as long a time as poss(1hr).It does progress a tiny bit further on each cycle but gets stuck at about 45%complete. Any suggestions?

Chowhound
Comic Vine
GameFAQs
GameSpot
Giant Bomb
TechRepublic