Actually there are two themes that are having troubles with MU. I think both use the same code for their links in the sidebar. Here is what is being used
<h3><?php _e('Links','bnOutThere'); ?></h3>
<?php
$link_cats = $wpdb->get_results("SELECT cat_id, cat_name FROM $wpdb->linkcategories");
foreach ($link_cats as $link_cat) {
?>
<h4 id="linkcat-<?php echo $link_cat->cat_id; ?>"><?php echo $link_cat->cat_name; ?></h4>
<ul>
<?php wp_get_links($link_cat->cat_id); ?>
</ul>
<?php } ?>
My db doesn't have a linkcategories for any blog. Should it? In fact it seems that things changed and I didn't notice but you don't have separate categories for links anymore. Any suggestions on how to alter the above to work with the new setup?