Look for IDE Cache fix in windows update:
ScanDisk Runs Even Though Windows Shut Down Correctly (Q273017)
--------------------------------------------------------------------------------
The information in this article applies to:
Microsoft Windows Millennium Edition
Microsoft Windows 98 Second Edition
--------------------------------------------------------------------------------
IMPORTANT : This article contains information about editing the registry. Before you edit the registry, make sure you understand how to restore it if a problem occurs. For information about how to do this, view the "Restoring the Registry" Help topic in Regedit.exe or the "Restoring a Registry Key" Help topic in Regedt32.exe.
SYMPTOMS
Although Windows may seem to shut down correctly, ScanDisk may run the next time you start the computer.
CAUSE
During the shutdown process, the contents of the virtual cache are written to the destination device. If the destination device isan Integrated Drive Electronics (IDE) hard disk, data may be written to the hard disk's onboard cache but not to the disk itself. When this occurs, the data is lost from the cache when the computer turns off.
RESOLUTION
To resolve this issue, you can download the Window IDE Hard Drive Cache package from the Microsoft Windows Update Web site at:
http://windowsupdate.microsoft.com
When the Windows Update page is displayed, follow these steps:
Click Product Updates to create the catalog of available updates for your computer.
After the catalog is created, click to select the Window IDE Hard Drive Cache Package check box.