I have such problem. I’m working with project, but when I copy the same files from server it looks different – some Bootstrap styling is not overrided.
Here is screenshots of working site header:

and what I see when opening THE SAME PROJECT on my computer:

I looked in Firebug and I see, that active link use this default Bootstrap styling:
.navbar .nav > .active > a,
.navbar .nav > .active > a:hover,
.navbar .nav > .active > a:focus {
color: #555555;
text-decoration: none;
background-color: #e6e6e6;
-webkit-box-shadow: inset 0 3px 8px rgba(0, 0, 0, 0.125);
-moz-box-shadow: inset 0 3px 8px rgba(0, 0, 0, 0.125);
box-shadow: inset 0 3px 8px rgba(0, 0, 0, 0.125);
}
So, as I see it is not overriding – WHY?
Try this: You should have a .scss (or .sass?) file to gather all the components. In MY case it is called styles.scss
The order in which the elements appear in this file is important – as the first entries overwrite the later ones – in case of variables! But put your styling(!) changes after your bootstrap entry.
My styles.scss file looks like this: