A few weeks ago, I don't know exactly when but definitely with or after the upgrade from 10.9 to 10.11 my Late 2013 iMac stopped being able to reboot or shutdown via the GUI. When I click a reboot button in an installer or in Finder, it just crashes to the black kernel panic screen.
This makes OS X updates impossible. I had to update from 10.11.0 to 10.11.2 via a complete install of OS X from the recovery console.
I can reboot via the reboot or shutdown commands in Terminal. But any attempt to shutdown or reboot from the GUI generates a kernel panic.
Any ideas?
Update
This is what installing OS X via the recovery partition did: