Use your browser's Developer Tools (F12), hit the inspect button, click on your dropdown (expand it before using the inspect button) and examine the CSS. You'll see that it's using var(--callToAction--hover)
which means that it's using the built-in themes.
For consistency in your app you should override these variables in the Project Browser | Perspective | Styles | right-click Advanced (I think) and then edit stylesheet.css.
Try adding this:
:root {
--callToAction--hover: #00cc00;
--callToAction--activeAlt: #dbe540;
}
Developer Tools should give you a list of all the theme variables on the bottom right and you may need to expand it. Click on a color and edit to find the settings you want and add those to your stylesheet.css overrides.