You feed power to the ignition circuit TWO ways ,from the battery (when starting) and from the battery, or/and,  one of the wires from the output of the voltage regulator ( when running). the problem stems from the fact that the wire from the regulator ties into the system AFTER the ignition switch ,so when you turn it off,  power is still being sent from the  regulator to power the bike.
  Generally that wire is tied into the orange wire leaving the ignition switch ,at the connector on the harness side, or into that line farther up. If you check at the regulator it should be one of the two wires other than yellow(3) or the black/white (ground) . find this wire an remove it to the red? wire (battery power)  going into the switch ,allowing the key to shut off both.