You could try a third party shutdown utility to see if it helps: click here
Troubleshooting startup and shutdown problems is difficult at best since so many things can be affecting the process.
Normally shutdown issues can be linked to software that us still running in the background and failing to correctly unload during the shutdown process.
Some people find that TweakUI click here can help in tuning their computer. Some people don't.
All I can suggest in the short term is that you try the Ctrl, Alt, Del key combination to call up the task manager. This will tell you which programs are currently running and if you list them in here one of us may be able to help. Windows 98 requires Systray and Explorer to run. Everything else is optional although you have to be very, very careful about disabling features since you could prevent antivirus software or firewall software from running.
One more utility that can help is Mike Lin's Startup Control Panel click here
This gives you an icon your Control Panel that allows quick and easy disabling of programs and services from your startup menu. It's easier to use than MSCONFIG and arguably more effective.
Finally, have you tried posting this in the helproom ? You'll more than likely get a larger audience in there than in the WebDesign forum.