This is strange, I had the shutdown issue with a fairly fresh install of Win 98 se
I installed the hard drive cache patch, Still hangs so I installed the shtdown supplement
It shuts down fine now, restarts fine, But when you want to restart in MS dos mode it goes to a black screen and just sits there, I could not use the ctrl+alt+delete, I had to hit the reset switch
Once we replaced a faulty floppy drive I could use the ctrl+alt+del to restart the system
SO all is fine unless you want to restart in MS dos mode
I can open a dos window and use the mem command, the ver command
They system is AMD based

a7v333 board
Athlon xp 2000+
Volcano 9 cooler
His video card
SB live 5.1 on it's own IRQ in pci slot 4
256 megs of brand name ran ddr 2100
300 watt psu
Win 98 SE