/**
 * Implements hook_theme_registry_alter().
 */
function module_theme_registry_alter(&$theme_registry)
{
    $theme_registry['status_messages']['function'] = '_module_status_messages';
}

/**
 * Custom theme function that overrides
 * theme('status_messages').
 */
function _module_status_messages($variables)
{
    global $theme;
    if($theme != 'theme_machine_name'){ // allow alert-boxes only in zurb theme

        return theme_status_messages($variables);
    }
    $display = $variables['display'];
    $output = '';
    $status_heading = array(
        'status' => t('Status message'),
        'error' => t('Error message'),
        'warning' => t('Warning message'),
    );

    // translate drupal core message types to zurb types
    $zurb_types = array(
        'status' => 'success',
        'warning' => 'warning',
        'info' => 'info',
        'error' => 'alert',
        'secondary' => 'secondary',
    );

    foreach (drupal_get_messages($display) as $type => $messages) {
        $output .= '<div data-alert class="alert-box ' . $zurb_types[$type] . ' radius">';
        if (count($messages) > 1) {
            $output .= " <ul>\n";
            foreach ($messages as $message) {
                $output .= '  <li>' . $message . "</li>\n";
            }
            $output .= " </ul>\n";
        } else {
            $output .= $messages[0];
        }
        $output .= '<a href="#" class="close">&times;</a>';
        $output .= "</div>\n";
    }
    return $output;
}