hello,
I didn't see where you close the first if statement. Seem like you have a nested if statement.
if (get_option(THEME_PREFIX . "twitter_link")) {
//twitter link
} --> try locate the closing bracket for the first if statement and append the new if statement below it.
if (get_option(THEME_PREFIX . "facebook_link")) {
//Facebook link
<li class="twitter"><a href="http://twitter.com/<?pho echo get_option(THEME_PREFIX . "twitter_link"); ?>"title"Twitter"></a></li>
//locate this
<li class="facebook"><a href="http://facebook.com/<?pho echo get_option(THEME_PREFIX . "facebook_link"); ?>"title"Facebook"></a></li>
>