Microsoft has issued a bug fix, humorously described as a "supplement," for Windows 98 Second Edition (SE), which addresses shutdown issues that certain users are having with the new OS. The "Windows 98 Second Edition Shutdown Supplement" is a 502 KB download that will prevent Windows 98 SE from hanging on shutdown or rebooting when it should have shutdown. If you're having either of these problems, you download the fix, which can be found on the Microsoft Web site.
Microsoft also recommends that you troubleshoot shutdown problems with Windows 98 SE before installing the supplement. You can find this information on its Windows 98 SE shutdown troubleshooter page