have you set the colors and LEDs for the layer indications you want?

from readme:

color_1=H,S,V
color_2=H,S,V

Set the colors used in backlight effects

caps_lock_indicator_color=H,S,V
layer_1_indicator_color=H,S,V
layer_2_indicator_color=H,S,V
layer_3_indicator_color=H,S,V

Set the color used for Caps Lock and active layer indicators

caps_lock_indicator_row_col=<ROW,COL|all|none>
layer_1_indicator_row_col=<ROW,COL|all|none>
layer_2_indicator_row_col=<ROW,COL|all|none>
layer_3_indicator_row_col=<ROW,COL|all|none>

Set the LEDs used for Caps Lock and active layer indicators.
ROW/COL specify which switch in the switch matrix

e.g.
ANSI Caps Lock Key:  caps_lock_indicator_row_col=0,2
Spacebar+stabs:      caps_lock_indicator_row_col=4,7
Esc Key:             caps_lock_indicator_row_col=0,0
Left Win Key:        caps_lock_indicator_row_col=4,1
Right Win Key:       caps_lock_indicator_row_col=4,11
Right Menu Key:      caps_lock_indicator_row_col=4,12
HHKB Fn Key:         caps_lock_indicator_row_col=3,13
All keys:            caps_lock_indicator_row_col=all 
None:                caps_lock_indicator_row_col=none

Note: Use layer_3_indicator_row_col=none if you use the default layer 3 keymaps which change the backlight.