To paraphrase the enhancement mod’s GitHub page (can be considered the de-facto instruction manual):
“Before you can change the palette register contents, you need to switch the output mode switch to a different mode and back again (back is optional).”
Switching between two modes/states/whatever can be referred to as ‘toggling’.
Your Ultimate Cart has no bearing on the issue (I have a first issue 1541U-II). Just toggle your mode select switch when instructed on screen and enjoy!