One suggestion, power-up the system, unplug the power and reset buttons from the motherboard then shut the machine down via windows. There is possible chance the power or reset buttons are sending a signal to cause machine to start back up. If the problem stops, plug in both again and start up then remove the reset button from the motherboard, shut down windows through windows and see if the system starts back up, if it doesn't start back up the reset switch is the culprit, if the system does start backup then possibly the power switch is the culprit. Do not use the switches to shut down, use Windows to shut down when troubleshooting this issue.
A few other possible problems are, a setting within Windows preventing shut down, this occurred in Windows 98/98SE on faster machines, which MS supposedly Fixed in Win2K and XP, or the ACPI/APIC is messed up within Windows itself, but I honestly think its a power switch problem.
Last Ditch Solution if none of the above work, try a different power-supply, higher rating, as I am unsure a 500 watt handles the machine properly- with the above troubleshooting tips in paragraph 1. Suggestion 2, remove the motherboard with the harddrive and powersupply and any other AGP/PCI/PCIe/USB brackets/cards, run them on a bench with the above trouble shooting tips in paragraph 1 and see if the problems stop- possible shorting in the case, or a card is making a connection with the case and motherboard, or the motherboard back side is touching the case.
