I am having the exact same problem. The demo Zen Cart storefront is up, but admin always routes to "System Setup Required".
Clean install of 1.3.9h, I've already deleted and reinstalled. I've checked and double checked everything in both configure.php files.
Edit: Database was also deleted and recreated between installations.
myDebug files reveal only the one error:
PHP Fatal error: Cannot instantiate non-existent class: notifier in /home/virtual/site10/fst/var/www/html/zencart/includes/autoload_func.php on line 79
I set a Debug Reporting variable to 'true', following advice I'd read from a similar thread. The following is output while accessing /catalog/index.php (which shows up just fine):
actionPoint=>0 include('/home/virtual/site10/fst/var/www/html/zencart/includes/classes/class.base.php');
actionPoint=>0 include('/home/virtual/site10/fst/var/www/html/zencart/includes/classes/class.notifier.php');
actionPoint=>0 $zco_notifier = new notifier();
actionPoint=>0 include('/home/virtual/site10/fst/var/www/html/zencart/includes/classes/class.phpmailer.php');
actionPoint=>0 include('/home/virtual/site10/fst/var/www/html/zencart/includes/classes/class.smtp.php');
actionPoint=>0 include('/home/virtual/site10/fst/var/www/html/zencart/includes/classes/boxes.php');
actionPoint=>0 include('/home/virtual/site10/fst/var/www/html/zencart/includes/classes/category_tree.php');
actionPoint=>0 include('/home/virtual/site10/fst/var/www/html/zencart/includes/classes/template_func.php');
actionPoint=>0 include('/home/virtual/site10/fst/var/www/html/zencart/includes/classes/split_page_results.php');
actionPoint=>0 include('/home/virtual/site10/fst/var/www/html/zencart/includes/classes/language.php');
actionPoint=>0 include('/home/virtual/site10/fst/var/www/html/zencart/includes/classes/cache.php');
actionPoint=>0 include('/home/virtual/site10/fst/var/www/html/zencart/includes/classes/sniffer.php');
actionPoint=>0 include('/home/virtual/site10/fst/var/www/html/zencart/includes/classes/class.phpbb.php');
actionPoint=>0 include('/home/virtual/site10/fst/var/www/html/zencart/includes/classes/shopping_cart.php');
actionPoint=>0 include('/home/virtual/site10/fst/var/www/html/zencart/includes/classes/navigation_history.php');
actionPoint=>0 include('/home/virtual/site10/fst/var/www/html/zencart/includes/classes/currencies.php');
actionPoint=>0 include('/home/virtual/site10/fst/var/www/html/zencart/includes/classes/message_stack.php');
actionPoint=>0 include('/home/virtual/site10/fst/var/www/html/zencart/includes/classes/breadcrumb.php');
actionPoint=>10 require('includes/init_includes/init_file_db_names.php');
actionPoint=>10 require('includes/init_includes/init_database.php');
actionPoint=>20 include('includes/version.php');
actionPoint=>30 $zc_cache = new cache();
actionPoint=>40 require('includes/init_includes/init_db_config_read.php');
actionPoint=>50 $sniffer = new sniffer();
actionPoint=>50 require('includes/init_includes/init_gzip.php');
actionPoint=>50 require('includes/init_includes/init_sefu.php');
actionPoint=>50 $phpBB = new phpBB();
actionPoint=>60 require('includes/init_includes/init_general_funcs.php');
actionPoint=>60 require('includes/init_includes/init_tlds.php');
actionPoint=>70 require('includes/init_includes/init_sessions.php');
actionPoint=>80 if (!$_SESSION[cart]) { $_SESSION[cart] = new shoppingCart(); }
actionPoint=>80 if (!$_SESSION[navigation]) { $_SESSION[navigation] = new navigationHistory(); }
actionPoint=>90 $currencies = new currencies();
actionPoint=>100 $template = new template_func();
actionPoint=>100 require('includes/init_includes/init_sanitize.php');
actionPoint=>110 require('includes/init_includes/init_languages.php');
actionPoint=>110 require('includes/init_includes/init_templates.php');
actionPoint=>120 $_SESSION[navigation]->add_current_page();
actionPoint=>120 require('includes/init_includes/init_currencies.php');
actionPoint=>130 $messageStack = new messageStack();
actionPoint=>130 require('includes/init_includes/init_customer_auth.php');
actionPoint=>140 require('includes/init_includes/init_cart_handler.php');
actionPoint=>150 require('includes/init_includes/init_special_funcs.php');
actionPoint=>160 $breadcrumb = new breadcrumb();
actionPoint=>160 require('includes/init_includes/init_category_path.php');
actionPoint=>161 require('includes/init_includes/init_canonical.php');
actionPoint=>170 require('includes/init_includes/init_add_crumbs.php');
actionPoint=>180 require('includes/init_includes/init_header.php');
I have tried to think it was my DIR_FS_CATALOG, etc. that were incorrect, but when I edit these to something intentionally wrong, the "System Setup Required" page actually alerts that DIR_FS... is invalid.
I have tried everything I can think of. I have installed an older version of Zen Cart with ABSOLUTELY no problems... Please let me know if I can provide any more information. Thanks.