You need to change the BIOS. There were a number of issues with shutdowns on Win98, especially SE. When the machine is booting, you'll see a flash of a screen saying to enter BIOS, hit F-8, I think. Sorry I don't have a Win98 machine running here. See if you can reset it. The screens will all have instructions, so it's pretty simple.
Geek babe, June 2005