Scandisk on windows 98 and ME will launch a window with a graphical display of the work it is performing. Sometimes, Scandisk will seem to stop and restart. This is because some other application is using the hard drive while Scandisk is attempting to diagnose it. If this happens ten (10) times, scandisk will report a failure and terminate without completing the scan.
This means that your system was busy doing something else at the time scandisk was trying to run.
Simply choose a different time to execute Scandisk. If your MS indexing is on, you may wish to temporarily suspend it, or select a time when the indexing isn't running to launch Scandisk.