NozlerAtClemson, don't worry about that "AT/AT COMPATIBLE" line under Computer on the System Properties dialog box. I have an ATX motherboard and power supply that I got in December, and it says the same thing for me.
When I tell Win2K to Shutdown, it does power off the machine. Your Win2K not doing that sounds like you might not be running the ACPI HAL. The first time I tried to install Win2K on this machine, it installed the Standard PC HAL and wouldn't power off the machine after a Shutdown, just like your machine is doing. Go to Control Panel->System->Hardware->Device Manager and then click on the + next to Computer near the top. If it says Standard PC rather than ACPI PC, that's probably why it's not powering down.
Before I reinstalled Win2K, I told the BIOS that I had a Plug and Play OS and turned on Power Management.