the theme also styles those more specific links:
.entry-content a:focus,
.entry-content a:hover,
.entry-summary a:focus,
.entry-summary a:hover,
.widget a:focus,
.widget a:hover,
.site-footer .widget-area a:focus,
.site-footer .widget-area a:hover,
.posts-navigation a:focus,
.posts-navigation a:hover,
.comment-metadata a:focus,
.comment-metadata a:hover,
.comment-metadata a.comment-edit-link:focus,
.comment-metadata a.comment-edit-link:hover,
.comment-reply-link:focus,
.comment-reply-link:hover,
.widget_authors a:focus strong,
.widget_authors a:hover strong,
.entry-title a:focus,
.entry-title a:hover,
.entry-meta a:focus,
.entry-meta a:hover,
.page-links a:focus .page-number,
.page-links a:hover .page-number,
.entry-footer a:focus,
.entry-footer a:hover,
.entry-footer .cat-links a:focus,
.entry-footer .cat-links a:hover,
.entry-footer .tags-links a:focus,
.entry-footer .tags-links a:hover,
.post-navigation a:focus,
.post-navigation a:hover,
.pagination a:not(.prev):not(.next):focus,
.pagination a:not(.prev):not(.next):hover,
.comments-pagination a:not(.prev):not(.next):focus,
.comments-pagination a:not(.prev):not(.next):hover,
.logged-in-as a:focus,
.logged-in-as a:hover,
a:focus .nav-title,
a:hover .nav-title,
.edit-link a:focus,
.edit-link a:hover,
.site-info a:focus,
.site-info a:hover,
.widget .widget-title a:focus,
.widget .widget-title a:hover,
.widget ul li a:focus,
.widget ul li a:hover {
color: #000;
-webkit-box-shadow: inset 0 0 0 rgba(0, 0, 0, 0), 0 3px 0 rgba(0, 0, 0, 1);
box-shadow: inset 0 0 0 rgba(0, 0, 0, 0), 0 3px 0 rgba(0, 0, 0, 1);
}
you need to take care of those as well.