The issue is that WordPress changed the menu code for WP 3.0. You could try the following.
Add the following line
HTML Code:
$list_pages_string = preg_replace("/<ul class='children'/","<ul",$list_pages_string);
Just before the following line in /functions/bfa_hor_pages.php near the top
HTML Code:
if ( $bfa_ata['page_menu_1st_level_not_linked'] == "Yes" ) {
You should make a copy of your bfa_hor_pages.php file first just as a precaution and double and triple check what you are copying and pasting. I only say that as I don't know how comfortable you are playing in the files. This is not a big deal to do but if you copy out too much or don't paste in the right place it can mess things up. Thus the copy of the file "in case"