Parmb,
If you're using Win98 Second edition (4.10.2222A), here's a link to the Shutdown Supplement:
If its installed and not working correctly,
The Fast Shutdown registry key may be enabled.
The Microsoft System Configuration utility includes an option to disable Fast Shutdown. If this option is unchecked in Windows 98 Second Edition, your system may reboot instead of shutting down.
To resolve this issue, backup the registry and/or export the following keys:
go to Start>Run, type regedit. Navigate to:
HKEY_LOCAL_MACHINE\System\CurrentControlSet\Control\Shutdown
Right-click on the FastReboot entry, choose modify and type in the number 0.
NOTE: When you apply the Windows 98 Second Edition Shutdown Supplement, which addresses shutdown issues, the Disable Fast Shutdown option is no longer listed on the Advanced tab in Msconfig.
In Win98 First Edition (4.10.1998), go to Start>Run, type msconfig, click the Advanced button and check Disable Fast Shutdown.
Try the Windows Shutdown Trouble-Shooter:
or the BIG one:
Microsoft Support Knowledge Shutdown articles
reghakr