If you run scandisk with your antivirus program running, it may not be able to complete. If you want to use scandisk from within Windows, simply <CTRL> <ALT> <DEL> and disable everything except systray. Then run it!

There doesn't seem to be anything wrong here except the way you're trying to use the tool. Scandisk for Windows 9x versions often won't work properly if anything is running in the background which tries to access the hard drive. The same problem crops up for Defrag as well.

This is a great little program to clost the thing running so you can run scandisk and defrag .
http://home.ptd.net/~don5408/toolbox/enditall/