I changed the top line to  1, 1, 1, and also tried assigning a bl mode and a bl enable key. I also tried some random settings on the led configuration menu and got the led 1 to light up if i set it as "usb ok" but if i set it as backlight it stays dark. 
Here is the current code i'm using for testing.
# Easy AVR USB Keyboard Firmware Keymapper
# Copyright (C) 2013-2016 David Howland
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License along
# with this program.  If not, see <http://www.gnu.org/licenses/>.
"""Keyboard definition for the Techkeys ThreeKeyBoard."""
import easykeymap.templates.ATmega16U2_16MHz_CARD as firmware
from easykeymap.ioports import *
description = "6KEY"
unique_id = "SIXKEY_001"
cfg_name = "SIXKEY"
teensy = False
hw_boot_key = True
display_height = int(3*4)
display_width = int(3*4)
num_rows = 1
num_cols = 6
strobe_cols = False
strobe_low = True
matrix_hardware = [
#     Port mask     Dir mask
    ( 0b10100000 , 0b00000000 ),    # REF_PORTB
    ( 0b10000000 , 0b00000000 ),    # REF_PORTC
    ( 0b01010010 , 0b00000000 )     # REF_PORTD
]
matrix_strobe = [
#     REF_PORTB    REF_PORTC    REF_PORTD
    ( 0b00000000 , 0b00000000 , 0b00000000 )
]
matrix_sense = [
#      Port        Pin mask
    
	( REF_PORTC , 0b10000000 ),
	( REF_PORTB , 0b10000000 ),
	( REF_PORTB , 0b00100000 ),
	( REF_PORTD , 0b01000000 ),
    ( REF_PORTD , 0b00000010 ),
    ( REF_PORTD , 0b00010000 )
]
num_leds = 7
num_ind = 0
num_bl_enab = 2
led_definition = [
    ('1', 'Backlight'),
    ('2', 'Backlight'),
    ('3', 'Backlight'),
    ('4', 'Backlight'),
    ('5', 'Backlight'),
    ('6', 'Backlight'),
    ('Underglow?', 'Unassigned')
]
led_hardware = [
#       Port    Pin    Direction
    ( REF_PORTC, 6, LED_DRIVER_PULLDOWN ),
    ( REF_PORTB, 6, LED_DRIVER_PULLDOWN ),
    ( REF_PORTB, 4, LED_DRIVER_PULLDOWN ),
    ( REF_PORTD, 5, LED_DRIVER_PULLDOWN ),
    ( REF_PORTD, 2, LED_DRIVER_PULLDOWN ),
    ( REF_PORTD, 3, LED_DRIVER_PULLDOWN ),
    ( REF_PORTC, 4, LED_DRIVER_PULLDOWN )
]
backlighting = True
bl_modes = [
    ( 1, 1, 1, 1, 1, 1 ),
    ( 1, 1, 0, 1, 0, 1 )
]
KMAC_key = None
keyboard_definition = [
    [((4, 4), (0, 0), 'HID_KEYBOARD_SC_A'),
     ((4, 4), (0, 1), 'HID_KEYBOARD_SC_S'),
	 ((4, 4), (0, 2), 'HID_KEYBOARD_SC_D')],
	 
	 
	[((4, 4), (0, 3), 'HID_KEYBOARD_SC_F'),
	 ((4, 4), (0, 4), 'HID_KEYBOARD_SC_G'),
     ((4, 4), (0, 5), 'HID_KEYBOARD_SC_H')],
    
]
alt_layouts = {}