htaccess rewrite to allow a new subdomain. - php

Question

I have a site I administer but I inherited the code from a previous developer. He wrote some rewrite rules, most of which seem to do the necessary job.
However my client has now purchased a subdomain eg: http://shop.thesite.com
However running this in the browser just returns http://thesite.com
I have tried commenting out some of the rules to try and get the shop subdomain to work, but I cannot seem to do it.
Here are the contents of the htaccess file:
DirectoryIndex index.php index2.php index.html index.htm
# For security reasons, Option followsymlinks cannot be overridden.
#Options +FollowSymLinks
Options +SymLinksIfOwnerMatch
RewriteEngine On
########## Begin - Rewrite rules to block out some common exploits
## If you experience problems on your site block out the operations listed below
## This attempts to block the most common type of exploit `attempts` to Joomla!
#
# Block out any script trying to base64_encode crap to send via URL
RewriteCond %{QUERY_STRING} base64_encode.*\(.*\) [OR]
# Block out any script that includes a <script> tag in URL
RewriteCond %{QUERY_STRING} (\<|%3C).*script.*(\>|%3E) [NC,OR]
# Block out any script trying to set a PHP GLOBALS variable via URL
RewriteCond %{QUERY_STRING} GLOBALS(=|\[|\%[0-9A-Z]{0,2}) [OR]
# Block out any script trying to modify a _REQUEST variable via URL
RewriteCond %{QUERY_STRING} _REQUEST(=|\[|\%[0-9A-Z]{0,2})
# Send all blocked request to homepage with 403 Forbidden error!
RewriteRule ^(.*)$ index.php [F,L]
#
########## End - Rewrite rules to block out some common exploits
# Uncomment following line if your webserver's URL
# is not directly related to physical file paths.
# RewriteBase /
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteCond %{REQUEST_URI} !^/index.php
RewriteCond %{REQUEST_URI} (/|\.php|\.html|\.xml|\.feed|\.ajax|\.img|\.xhtml|/[^.]*)$ [NC]
RewriteRule (.*) index.php [L]
#RewriteRule .* - [E=HTTP_AUTHORIZATION:%{HTTP:Authorization},L]
<Files *.inc.php>
order allow,deny
deny from all
</Files>
<Files pagecounter.inc.php>
order allow,deny
allow from all
</Files>
<IfModule mod_php5.c>
php_value upload_max_filesize 50M
</IfModule>
<IfModule mod_php4.c>
php_value upload_max_filesize 50M
</IfModule>
I realise that is alot of code, and this is probably not the most enlightened question, but I would appreciate some help.
This was the line that I thought was rewriting the subdomain:
RewriteRule (.*) index.php [L]
I did comment that out but it made no difference, so now I am also wondering if I am having to deal with any caching issues.