There are several reasons for Win98se to not shut down properly, read at the following Microsoft site concerning the possible fixes. If the computer is configured to have a shutdown sound...i.e.. some wave sound when/as Windows closes/..this can cause Windows not not complete its shut down at times, especially if the wave file is corrupt in any way. Just turn off any shutdown wave sounds as the machine is exiting.
http://support.microsoft.com/default...;en-us;Q239887
Be sure to disable fast shut down in msconfig. (ooopsss I just saw you had said the same Bill...BTW...what happened to the IDE ribbon cable swapout and the HDD problem you had awhile back?)