I'm using a 2-port KVM switch between my Mac Mini and a Ubuntu desktop computer. I have no problems with the Ubuntu machine waking up when I switch to the inputs. However, when I switch over to the Mac Mini, the monitor stays dark.
This problem only started after upgrading the Mac Mini to OSX 10.11 El Capitan.
FWIW: When I VNC in from another computer, the monitor fires up just fine and I can do stuff just fine. Then I can use the keyboard and mouse hooked up through the KVM switch on the Mac Mini.
Also, I am switching using the physical buttons on the KVM switch; not a hotkey sequence on the keyboard.