Oh! Always a trouble, auto-poweroff on shutdown. But a fixable problem :-D
I guess you'll need to experiment a little. Different computers have different settings. You'll want to append options to the kernel.
By setting acpi=force to the kernel, my computer gets auto-poweroff enabled, but looses access to the USB ports.
By appending pci=noacpi, I fix this. Everything works great now. So in grand total, I've put this in lilo.conf:
append = "acpi=force pci=noacpi"
Note however that this may be different on your machine. Try to append the above one at a time, and watch what happens. Do you know how to append kernel options?