2012 Mac Pro 12-Core OSX El Capitan hangs at logout, restart and shutdown

Hi. Anyone have this problem and found a fix?
I have a 2012 Mac Pro 12 Core 3.46GHz running El Capitan and recently I can't logout, restart or shut down.
I've tried zapping PRAM, shutting down, unplugging, remove battery, etc. and nothing works.
I've run Apple's disk utility and the PCIe SSD boot drive is fine.

Here is what happens when I go to power up again:

I shut down with the power button restart and then it goes through it's normal procedure:

Then status bar shows progress half way

Then the computer fans sound like they power down

Then it goes to blank grey screen with selection arrow at top left

then a minute later a small error message saying you shut down because of a problem....,

I hit ok and then to the desktop and all is good.

Apps and everything else work fine, etc.

Any help is greatly appreciated.
Pat

Boot in to Recovery and see if that is available. Then run Disk First Aid.

Also try cold booting but using Safe Boot Mode. Then when booted and logged in, maybe run what you can with Disk Utility and then reboot normally and see if things improve.