win98 shutdown

I think Microsoft has at least 3 patches for your problem have you tried those already? what programs are selected for autostart? do you have a config.sys specified and what's in it? are there any commands executed by the autoexec?
These are just afew question but it can be anything. are all your system the same config? sometimes you have to specify EMM memory but exclude the dos video page. Soome antivirus programs try to use this part of the memory and the two will be fighting over it resulting in a lock up during shutdown

Microsoft has patches, but there are numerous causes for the problem. You have to narrow down the parameters. See...

http://www.aumha.org/a/shutdown.htm

Microsoft's patches are a good start, but I've found they don't fix all our problems. The troubleshooter will walk you through other solutions:
http://support.microsoft.com/support/kb/articles/Q238/0/96.ASP
(remove spaces from url)
I've found that about 90% of the time, my problems were with sound card drivers, and updating these solved the issue.