|Have the switches previously worked as they should? If not, then the case to motherboard wiring may not be connected correctly. |
ATX power switches are momentary contact type. If the switch is sticking in, that can cause problems. I have one that occasionally sticks in.
The BIOS settings in the BIOS for the computer I am currently using has a setting in Power Options to determine how the computer is shut down.
Going back to how you need to shut down, are you stating that you can't go to Start> Turn off computer, and use that to shout down?