Shutdown problems in Windows 98 Second Edition can be caused by any of the following issues:
The Fast Shutdown registry key is enabled.
There is a damaged Exit Windows sound file.
A program or terminate-and-stay-resident (TSR) program may not close correctly.
An incompatible, damaged, or conflicting device driver is loaded.
There is an incompatible Advanced Power Management (APM) or Advanced Configuration and Power Interface (ACPI) setting.
There is an incompatible BasicInput/Output System (BIOS) configuration setting.
The computer contains incorrectly configured or damaged hardware.
There is a video adapter that is not assigned an IRQ in real mode.
----------
IRQ Steering:
This option allows several PCI devices to share the same interrupt request line (IRQ). If the BIOS is not fully compliant, this option may cause your computer not to shut down properly, even if two or more devices are not sharing an IRQ. To disable PCI bus IRQ Steering, follow these steps:
Click Start , point to Settings , click Control Panel , and then double-click System.
On the Device Manager tab, click System Devices.
Double-click PCI Bus , and then click to clear the Use IRQ Steering check box on the IRQ Steering tab.
Click OK , click OK , and then restart your computer.
After you restart the computer, attempt to shut down your computer again.
If your computer shuts down successfully, you may need to change the BIOS configuration or you may need a BIOS update. For information about how to do so, contact your BIOS manufacturer.
(continued in comments...)