I brought this problem up in another thread (see "w98se setup -- Bad Fault in MS-DOS Extender") and I thought it was interesting enough to deserve its own thread. Besides, if a problem is brought up on a forum, it is nice to eventually see the solution/conclusion. So here goes ...
After installing W'98se on my latest Frankenstein PC (see some of my other posts in these forums), the machine will not shut down. It hangs with the shutting-down display on the screen. Fortunately, it doesn't appear to cause problems if the power switch is used after a minute without activity.
The Microsoft Knowledge Base has quite a bit of information on this (Q238). It seems like this article is saying that virtually any piece of software that is running or hardware that is enabled could be causing the problem, and there is lots of advice for troubleshooting. If you are like me, and apparently many are because they gave me the following advice, you won't want to go through the witch hunt and will instead want to download the Shutdown Supplement (Shutdown Supplement), which is supposed to fix the problem. Unfortunately, the supplement did not work for me and I will have to engage in the witch hunt.
Since I did a clean installation of Windows and because the problem surfaced before I started loading applications, many of the potential sources of trouble are eliminated. The most suspicious areas are the hardware and the BIOS settings, particularly those associated with power management and IRQ steering. Any help would be appreciated.