Hello,
I had the same issue with the index.html file repeating the Flash intro over and over again. I ended up re-naming the page intro.html and it solved the repeat issue.
Then in order for the intro.html page to load at the main URL, and load only once, I changed the index.php file to this:
<?php
session_start();
if(!isset($_SESSION['flashIntroShown']))
{
$_SESSION['flashIntroShown'] = 1;
header('Location: https://yourwebsiteURL.com/intro.html');
}
define('WP_USE_THEMES', true);
require('./wp-blog-header.php');
?>
I didn’t have to make any changes to the rest of the wordpress site. Hope that helps!