Zastosowałem się do wskazówek autora i podświetlenie oraz LED notifications działają jak należy.
" The problem looks to be that peoples preferences are slightly broken. For people having problems, you can do one of three things:
Uninstall the app, and then reinstall.
Toggle all the preferences on/off and then reset them to what you want.
Delete the preferences file (see below for the command), and then reset them to what you want. "