gbtravel Hi
The "Brand primary color" is coming right as envisaged however, there is conflict coming from another CSS rule-set due to which the specific CSS property is being superseded henceforth not applying. Ref: Screenshot
Try add this to custom.css file and the same shall apply :
.nav-pills > li.active > a{background:#fe6945 !important;}
Kindly ensure to clear your browser cache if changes dont reflect.
Note: You may disable css compression while the site is still in development phase, in order to get the right CSS file reference where the CSS rule-sets can be seen coming from henceforth making it easier for debugging purposes and provide more concise solution