setting colors in editor
If it seems not to be working as it should for .js files, and in the unlikely event that it hasn't already been done, I would be inclined to check that, after making the changes wished for, OK is clicked on the Highlighting panel and then on the Preferences panel. My experience is that such changes are effected on that second click.
If that doesn't do the trick, I would request the help of the CoffeeCup team at https://www.coffeecup.com/help/myroom/ .
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