ACPI 2.18 now properly turns the power off completely when I use Xshutdown -> shutdown only. Earlier versions didn't do this; apparently they were putting the system into a sleep mode, because the power LED stayed lit even though the computer seemed to turn off. So this is good progress.
However, every time I use this method, CHKDSK runs on all disks when I reboot. I have the "Delay" checkbox checked on the XShutdown tab, but that only waits for 3 seconds.
So, does XShutdown need a longer delay, or is ACPI somehow not telling the drives to shutdown properly?
Tyan motherboard with Athlon 64 X2 + nForce4 chipset.