This fix is the one that worked for me with a similar set-up to yours:
"Similar problem on an iMac running El Capitan 10.11.2 which didn't immediately get resolved by the SMC reset. However, after much frustration, I decided to leave the iMac unplugged overnight as part of the reset process. In the morning I pressed the power button prior to reconnecting the mains as this is recommended in various place, plugged in the power and switched on with wired keyboard now attached and all worked. Prior to this I had various levels of success using a straight usb extension on the keyboard and that worked on all but one of the USB ports but I couldn't plug the keyboard in directly. A USB mouse in this port did not light up either but did in the other ports so it led me to believe that the SMC reset was capable of making a difference but the system needed a lot longer to drain any residual capacitance thus the overnight wait."