Try this:
http://www.uvsc.edu/helpdesk/faq/win...downpatch.html

While you're at the Update site, make sure you've got all the Critical Updates installed!

I went to that web site and it is for windows98 second edition. I have the firsr edition so I don't think that will work. Are there any other suggestions?

Quite likely, this is actually a hardware problem, either a loose board/dirty contact in the system itself or a corrupted driver ("slow" = "old" so dust/dirt can cause problems). At shutdown, each hardware device "signs off." If the board has a dirty contact (for example) or a corrupted driver it can't always properly acknowledge the shutdown command. It's still possible for it to boot up and run normally in this situation. First, check that all boards are properly seated in their sockets. Second, it's not a bad idea to pull each board and clean the edge-contacts with isopropyl alcohol, 91-99% pure (70% rubbing alcohol is not appropriate; an isopropanol "drygas" such as Iso-HEET works well for this). Last, check to ensure that all drivers are as up-to-date as possible.

That basically just leads you to the Windows Update site, go there and get all your Critical Updates and see if there is one that says Shutdown Patch.

Thank you sooo much TallCool1. It worked. I looked inside and there didn't seem too much dust so I went exploring and carefully took apart my power supply. It had layers upon layers of dust. I blew it out put my computer back together, booted and then rebooted. The reboot was the fastest I have seen my computer do in years. I think everything is running faster. Thankyou so much. I didn't know what to do.

Same thing has happened in my pc with a little difference.It is responing to retart command only but not in shut down command and start indos mode command.It hangs in the the midway with the message"windows is shutting down".My pc is p3 with win 98se ATX.Please help me also.