There is a shutdown supplement available through Microsoft that may help you. Here is a portion of the article:
Windows 98 Second Edition Shutdown Supplement (Q239887)
SYMPTOMS
You may experience any of the following symptoms when you select an option in the Shut Down Windows dialog box.
If you click Shut down or Restart in MS-DOS mode and then click OK with fast shutdown enabled, the computer may restart instead of shutting down.
CAUSE
This problem can occur because:
The computer could hang at the shutdown screen intermittently, because the Apmbatt.sys component is not responding to the system shutdown notification from the operating system and could enter an endless loop.
-or-
The computer could hang with a black screen because of the method in which IRQ holders for the video adapter are configured at boot time and disabled during shutdown by the Pci.vxd component.
-or-
The fast shutdown option modified by Msconfig.exe contains a code path in which the computer could reboot instead of properly shutting down or quitting to MS-DOS.
NOTE : The Shutdown Supplement was updated 11/99 to address a newly discovered issue that allowed continued shutdown failures on some Windows installations. Due to the added functionality in the update, it may appear on Windows Update as not installed, even if the original version of the Supplement was previously installed.
RESOLUTION
The Windows 98 Second Edition Shutdown Supplement addresses shutdown issues on computers with specific hardware and software configurations running Windows 98 Second Edition.
You can download and install the Windows 98 Second Edition Shutdown Supplement file at: http://www.microsoft.com/windows98/downloads/contents/wurecommended/s_wufeatured/win98se/ or http://www.microsoft.com/windows98/downloads/corporate.asp
I have also reinstalled Windows98SE and solved the problem. Hope this helps.
Dana
