See Microsoft article Q238096 titled, "Problems Shutting Down Windows 98 Second Edition"
This article describes how to troubleshoot shutdown and restart problems in Windows 98 Second Edition specifically, not Microsoft Windows 98. For additional information about troubleshooting Windows 98 shutdown problems, click the article number below to view the article in the Microsoft Knowledge Base:
The following topics are discussed in this article:
Windows 98 Second Edition Shutdown Supplement
Troubleshooting
Common Causes of Shutdown Problems
Known Issues
IRQ Steering
Resume on Ring and LAN
Plug & Play BIOS
NVRAM/ESCD
Fast Shutdown Registry Key Is Enabled
Antivirus Program
Replacing the Configmg.vxd File
Functions Performed During the Shutdown Process
See this link:
http://support.microsoft.com/default.aspx?scid=kb;EN-US;q238096
(REMOVE SPACES from the pasted URL)
Most times, I've seen that disabling the fast shutdown will solve the problem. However, you should review the entire article.
Good luck,
Maxwell