I have been battling this bizarre problem for over a month, and after lots of detective-work, I now suspect a Windows Update from last January to be the cause.
Briefly, since about a month ago, I suddenly can no longer Shutdown/Reboot from Windows (I must use the buttons on my PC to complete the task.) Note, problem does not occur in Safe Mode or Linux.
I've found that if I disable the driver for my video card (GTX670 in a PCIe slot) or ONE particular driver related to my TV tuner (ATI HDTV Wonder in a PCI slot), everything works fine again. But neither (obviously) is a permanent solution.
With some more experimenting, I discovered that if I rollback one or both of a particular Intel Device driver, I can Shutdown/Reboot ONCE. And upon returning, if I put BACK those drivers, I can Shutdown/Reboot ONCE one time more. Extremely odd.
Checking my "Windows Update" History, this particular update (INTEL - System - 10/3/2016 12:00:00 AM - 10.1.1.38) is the last hardware related update installed back in January. There is no KB number, no information on what changes it made, and no info on how to undo it (as I mentioned, rolling back the driver only helps one time.)
Does anyone know what changes this update makes and how to undo them?
TIA.