In certain parts of my text, when I do apply underline, the color of the underlining is light grey (barely visible) even though the font is black. I searched different places to change the color of the underline. Tried the ‘Show Font’ window where the underline menu button at the tops has a ‘color’ item but there the selected color is black and will only influence the color of the second underline when applying ‘double’ underlining (the first underline is still light grey).
I’m not aware of anything else you need to be doing. Are you getting the same result if you paste the text into TextEdit and then try the same exact thing from there? If not, maybe try restarting Scrivener—these system palettes can sometimes get confused, and maybe the colour palette is no longer “talking to” the font palette.