Hello hotkee, I've checked both and they're identical. I "upgraded" to beta 3 of the WP 2.6, so the index.php is the same as the install default. My FTP server said that my htaccess was modified yesterday, but I don't see any glaring differences.
.htaccess contents:
DirectoryIndex index.php
AuthName rishi-kumar.com
# BEGIN WPSuperCache
<IfModule mod_rewrite.c>
RewriteEngine On
RewriteBase /
AddDefaultCharset UTF-8
RewriteCond %{REQUEST_METHOD} !=POST
RewriteCond %{QUERY_STRING} !.*s=.*
RewriteCond %{QUERY_STRING} !.*attachment_id=.*
RewriteCond %{HTTP_COOKIE} !^.*(comment_author_|wordpress|wp-postpass_).*$
RewriteCond %{HTTP:Accept-Encoding} gzip
RewriteCond %{DOCUMENT_ROOT}/wp-content/cache/supercache/%{HTTP_HOST}/$1/index.html.gz -f
RewriteRule ^(.*) /wp-content/cache/supercache/%{HTTP_HOST}/$1/index.html.gz [L]
RewriteCond %{REQUEST_METHOD} !=POST
RewriteCond %{QUERY_STRING} !.*s=.*
RewriteCond %{QUERY_STRING} !.*attachment_id=.*
RewriteCond %{HTTP_COOKIE} !^.*(comment_author_|wordpress|wp-postpass_).*$
RewriteCond %{DOCUMENT_ROOT}/wp-content/cache/supercache/%{HTTP_HOST}/$1/index.html -f
RewriteRule ^(.*) /wp-content/cache/supercache/%{HTTP_HOST}/$1/index.html [L]
</IfModule>
# END WPSuperCache
# BEGIN WordPress
<IfModule mod_rewrite.c>
RewriteEngine On
RewriteBase /
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule . /index.php [L]
</IfModule>
# END WordPress
index.php
<?php
/**
* Front to the WordPress application. This file doesn't do anything, but loads
* wp-blog-header.php which does and tells WordPress to load the theme.
*
* @package WordPress
*/
/**
* Tells WordPress to load the WordPress theme and output it.
*
* @var bool
*/
define('WP_USE_THEMES', true);
/** Loads the WordPress Environment and Template */
require('./wp-blog-header.php');
?>