I'm using Atahualpa 3.4.4 with WordPress 2.9.2. I made the change on line number 119. Here is the html along with the previous few lines.
HTML Code:
// Logo Area
if ( strpos($header_items,'%logo') !== FALSE ) {
$logo_area = '<table id="logoarea" cellpadding="0" cellspacing="0" border="0" width="100%"><tr>';
if ( $bfa_ata['show_search_box'] == "Yes" AND ($bfa_ata['show_posts_icon'] == "Yes" OR
$bfa_ata['show_email_icon'] == "Yes" OR $bfa_ata['show_comments_icon'] == "Yes") ) {
$header_rowspan = 'rowspan="2" ';
} else {
$header_rowspan = '';
}
// Logo Icon for Wordpress and WPMU
if ( $bfa_ata['logo'] != "" ) {
$logo_area .= '<td ' . $header_rowspan . 'valign="middle" class="logoarea-logo"><a href="http://www.shop.thegameacademyonline.com/"><img class="logo" src="';