If by primary you mean bottom menu ( and by secondary the top menu), there is currently a 4px top border and 1px bottom border on the header image with the rule
#header #branding img {border-top: 4px solid #000;border-bottom: 1px solid #000;clear: both;display: block;}
If you added that rule remove it. If you did not, it may have come with a sub theme you used, in which case the rule is probably in Main Options > Fonts & Custom > Custom CSS Rule box. It could alo be in one of the CSS+ boxes in the Main Options > HEader page.
If you meant the reverse, the bottom menu bar is set to have a border with the option found in Main Options > Menus