#Technically, it's bydesign. But really, it's just godawfuldesign.
The bright borders are part of the background:
The dark borders, on the other hand, are defined in the CSS:
.nav li {
border-left: 1px solid rgba(160, 50, 10, 0.3);
float: left;
margin: 0;
padding: 0;
}
These don't align properly (yay boxmodel, random changes and stuff like that) and as such, this bug occurs.