Make sure you have correctly setup the Device Shutdown Procedures within the BIOS.
A device may be bringing the system out of its "Power Off" state, a PCI device for example (this can also influence a total power off position).
I suggest you look within the BIOS and prevent such devices from bringing the system out of its "Power Off" state. You will also need to make sure you prevent Power on State(s) when AC/DC power fails.
Memory module issues can prevent the system from powering off.
This is a problem with the design of the x86 architecture (current design).
The x86 design states that if the Memory is still transferring data, regardless of size, the system will not automatically activate a Power Off state.
A damaged memory module can, and often will, be transferring data to the AGU system, therefore this will prevent the system from powering off.
I suggest that you use a trial and error method to ascertain if one (or both) of your memory modules are having problems.
If neither of these work I suggest you reduce the Voltage to the CPU and decrease the clock as low as possible, for test purposes.
Certain Power Supply Units will have problems with powering off if they are operating outside of their design, i.e. more power draw than design states.
I have noticed this with my old 220W PSU in one of my PC's. When the peak is breached slightly the system does not power off correctly, and I have to turn it off manually using the Power Off button.