That's somewhat normal. Most if not all of the intelligent power supplies don't know if the PC is on or off.
All they do is sequence the startup and shutdown. When IGN goes high, turn power on, pulse power button and ignore any change for several minutes. When IGN goes low, pulse power button, wait several minutes, turn power off.
So when you shut down manually, the PSU just assumes the PC is running. Turn IGN off and it will pulse the power button and wait a few minutes to turn the power off even though it just booted the PC. D'Oh!