1. CSS/HTML issues are off-topic for this site, per the FAQ.
But, have you tried investigating with Firebug or Chrome’s dev tools? The answer is obvious in seconds. This page http://www.biz.uiowa.edu/bta/test/ has large headings because of
.singular .entry-title {
font-size: 2em;
margin-bottom: 0.3em;
}
Since you are running a second loop on a singular page, the body class issue I proposed in the comments is catching you.
2. To best exclude a category from the index loop you should use pre_get_posts
.
function wpa_94196_exclude_category( $query ) {
if ( is_home() && is_main_query() ) {
set_query_var( 'cat', '-9' );
}
}
add_action( 'pre_get_posts', 'wpa_94196_exclude_category' );