Question is, why are you tring to tackle this puzzle without a central connecting php script?
As codezilla has already said, in my words - because it's a pain in the a$$. My own site uses that approach - I used the 2.x version to ezpublish to build it. It has advantages in that you can give alot of power to the apps user without needing to write any PHP but the price is flexibility. If I want to use phpBB as the forum for phppatterns, the first hurdle I have to overcome is how phpBB will fit with being accessed via index.php.

This comes back to my opinion that Apache is PHP's front controller. Considering that example I posted above;

PHP Code:
<?php
// index.php

switch ( @$GET['module'] ) {
    case 
'news':
        include 
'news.php';
    break;
    case 
'forum':
        include 
'forum.php';
    break;
    default:
        
header('http/1.1 404 Not Found');
        die(
'Page not found');
    break;
}
?>
I can eliminate that script and my app should keep on working - news.php and forum.php being passed the requests directly from Apache.

The other issue with a central script is, unless you're careful (e.g. using the filesystem to check a page controller exists), it leads to slow down while PHP wades through something like a massive switch statement.