I had the same problem with a 98 desktop PC. This worked:
This is from the Microsoft Website:
When you shut down Microsoft Windows 95 or Windows 98, all device drivers are uninitialized. If fast shutdown is enabled in Windows 98, device drivers are not uninitialized. This results in a faster shutdown. Fast shutdown is enabled by default. Disabling fast shutdown may be necessary when you are troubleshooting shutdown problems in Windows 98.
To disable fast shutdown, follow these steps:
Click Start , point to Programs , point to Accessories , point to System Tools , and then click System Information .
On the Tools menu, click System Configuration Utility .
On the General tab, click Advanced .
Click to select the Disable Fast Shutdown check box, click OK , and then click OK .
Click Yes when you are prompted to restart your computer.
Disabling fast shutdown in Windows 98 changes the FastReboot value data from 1 to 0 in the following registry key:
HKEY_LOCAL_MACHINE\System\CurrentControlSet\Control\Shutdown