Hi,
The reason the plugin does that is because there isn’t enough color contrast between the background and text colors there (according the color contrast calculations and standard accessibility guidelines). Unfortunately, your color scheme (which is cool, by the way!) doesn’t lend itself to this approach since the gray color is hard to achieve contrast with by going lighter.
You should add the following css via a custom css plugin to override that part of the code:
/* Override higher contrast Accent Color against contrast color */
.site-navigation .current_page_item > a,
.site-navigation .current_page_ancestor > a,
.site-navigation .current-menu-item > a,
.site-navigation .current-menu-ancestor > a,
.site-navigation a:hover,
.featured-content a:hover,
.featured-content .entry-title a:hover,
.widget a:hover,
.widget-title a:hover,
.widget_twentyfourteen_ephemera .entry-meta a:hover,
.hentry .mejs-controls .mejs-button button:hover,
.site-info a:hover,
.featured-content a:hover {
color: #ff0000;
}
.hentry .mejs-controls .mejs-time-rail .mejs-time-current,
.mejs-overlay:hover .mejs-overlay-button,
.slider-control-paging a:hover:before,
.slider-control-paging .slider-active:before,
.slider-control-paging .slider-active:hover:before {
background-color: #ff0000;
}
But you might want to try a different color for these particular ones, since the red ends up being a bit difficult to read.