Its to general Q. The best way is to "inspect" element and check for "conflicts".

1) Maybe you add in your style !important or more specific "background-color" style - inline for example, more CSS file (last win). Example:
"blue" win.

2) From "less" view - you can "check" the compile value in your CSS (Change? not change?) - with Control+F (change to "red" and check the css code). I believe yes.

3) Maybe the custom template or your theme you dont have any class "selector" for background. I dont use this template, or elemental to answer this specific.

4) Clear cache issue

Thanks for your reply. I've managed to do it using manually-entered CSS, but I don't think I should have had to. I'm surprised that none of the Theme->Customise options did the trick. Those work for drop-down sub-menus, but not the main menu bar (unless I'm missing something).

I think the customizer depent on the markup. If you work with new custom template its not always match (unless you use the correct less vars in your selectors).

Learn about this issue in C5 docs.