I built a desktop a year or so ago, which runs like a dream. I have installed many OSes on it but the problem persists. If it tell the PC to restart it does everything right, shuts down but the PC remains on before it can restart. The OS shuts down and nothing is running, but the desktop stays on. If it helps, the PC shuts down fine. Just an annoying issue if I get updates in Windows/ Ubuntu etc.
Couple things to try: