With my new installation I have the same problem. Shutdown just reboots every time.
Manual sleep, via the apple menu makes my rig go to sleep but it wakes up immediately,
behavior same as shutdown.
Normal sleep works as well however it is impossible to wake the computer, only a reboot
with the power button allows me back in to the machine.
The cause, in my case is the USBinject all kext, after removing that the machine works as
intended with one exception, upon waking from sleep I loose audio and have to reboot to
get it back. Even running "sudo killall coreaudiod" which restarts the audio subsystem,
does not fix it so a reboot is all that will get audio back.
I am still working on a solution and would appreciate some advice and help.
For my new rig in the making I use the following components:
Mobo: GA-Z170-Gaming K3, Mem:4 x 8 gig Patriot DDR4-2600 Cooling: Corsair Hydro H100i (2)
PSU: Cougar modular 750 Watt, GPU: Nvidia GTX 970, Cpu: Skylake i7-6700K