I have this problem , I have to go through the "Shut Down" twice before it will shut down. The same with restart and "Sleep " mode.
I seem to have done everything offered by MS and the web. I have also checked the "Fast Shutdown" in the Registry to Zero (there were 2 one a default, so I am NOT sure if that is correct) anyone any idea please. ??
Its weird I have to go through the shutdown proceedure twice and no more.
So many things can be the culprit with Windows 98/98SE shutdown and startup it is almost impossible to diagnose in general discussion like we do in this forum.
I've seen a corrupt sound file cause havoc when a computer was trying to close down. It really can be something that simple.
All I can suggest is probably what you have already tried, use the task manager to see what is running just before and during shutdown.
Disable everything in the machines startup panel via MSCONFIG other than Explorer and Systray - evern get rid of any antivirus or firewall software you run, just as an experiment to see if something is failing to unload during shutdown. Re-enable your AV and firewall as soon as you have tried and verified this.
Likewise, disable Windows sounds completely, just for the sake of curiosity. You can always select a sound scheme again later.
If you run Task Manager just before shutdown and verify that nothing is running, then watch it closely when you select your shutdown option, you may get a clue.
Finally, have you investigated the bootlog option for Windows 98 ?
You can read a bootlog and run a bootlogged startup to see if anything is failing to load correctly when being called by the system. This is normally used for startup issues, but can also sometimes indicate more general problems that may have more far reaching consequences. Anything that is an issue in your bootlog will be in the last few lines of the textfile, so you don't have to pore through the entire log.
My apologies if you have already done all of the above.