Scan Disk Locking up

I have a computer connected to a peer to peer network that is running scandisk due to improper shutdown. Scandisk is launching at startup and will lock up at about %40 when doing the surface scan.

I figure my next move is to run scandisk directly from the Win98 CD.

Immediately before encountering this problem I uninstalled Norton (expired subscription) and Installed AVG Free Edition.

I was suspicious that the AVG may be interfering with the surface scan so I uninstalled AVG but the scan still locks up.

The OS does load and seems to work so long as scandisk is aborted before it locks.

This is a clients computer and they use it to throughout the day to run line of business applications. It is not a server but it is the primary point for data entry into a custom database program that is installed. i don't want to take any dratic steps that may interfere with this program. I have been told it is quite finick. Since it is working I am trying to be judicious in my steps. Also the computer seemed to be working fine before the install of the AVG.

I expect that running scandisk from the cd will repair a disk error but I would like to be prepared for anything.

Any thoughts or suggestions?