In the .kobo/Kobo/Kobo eReader.conf file under the FeatureSettings heading, did you add either DarkMode=true or InvertScreen=true?
Code:
[FeatureSettings]
DarkMode=true
InvertScreen=true
Personally, I'd suggest adding NickelMenu with either Dark Mode or Invent Screen or both of them. You can add this multiple times under main, library, reader, etc.
Code:
#
menu_item : main : Dark Mode : nickel_setting : toggle : dark_mode
menu_item : main : Invert & Reboot : nickel_setting : toggle : invert
chain_success : power : reboot
#
Note that Invert Screen needs a reboot to apply.