cPanel reliese on the .htaccess file found within /public_html to redirect the websites. However Joomla's .htaccess settings interfer with cPanels. So the solution is to move cPanel's code above Joomla's and below the line

RewriteEngine On

An example of this is

##
 

# @version $Id: htaccess.txt 10492 2008-07-02 06:38:28Z ircmaxell $
# @package Joomla
# @copyright Copyright (C) 2005 - 2008 Open Source Matters. All rights reserved.
# @license http://www.gnu.org/copyleft/gpl.html GNU/GPL
# Joomla! is Free Software
##

#####################################################
# READ THIS COMPLETELY IF YOU CHOOSE TO USE THIS FILE
#
# The line just below this section: 'Options +FollowSymLinks' may cause problems
# with some server configurations. It is required for use of mod_rewrite, but may already
# be set by your server administrator in a way that dissallows changing it in
# your .htaccess file. If using it causes your server to error out, comment it out (add # to
# beginning of line), reload your site in your browser and test your sef url's. If they work,
# it has been set by your server administrator and you do not need it set here.
#
#####################################################

## Can be commented out if causes errors, see notes above.
Options +FollowSymLinks

#
# mod_rewrite in use

RewriteEngine On

##################

# This is cPanel's redirection code from joomlawired.com to joomlawired.co.uk

##################
RewriteCond %{HTTP_HOST} ^joomlawired.com$ [OR]
RewriteCond %{HTTP_HOST} ^www.joomlawired.com$
RewriteRule ^(.*)$ "http\:\/\/www\.joomlawired\.co.uk\/$1" [R=301,L]

########## 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 set a mosConfig value through the URL
RewriteCond %{QUERY_STRING} mosConfig_[a-zA-Z_]{1,21}(=|\%3D) [OR]
# 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.
# Update Your Joomla! Directory (just / for root)

# RewriteBase /

########## Begin - Joomla! core SEF Section
#
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteCond %{REQUEST_URI} !^/index.php
RewriteCond %{REQUEST_URI} (/|\.php|\.html|\.htm|\.feed|\.pdf|\.raw|/[^.]*)$ [NC]
RewriteRule (.*) index.php
RewriteRule .* - [E=HTTP_AUTHORIZATION:%{HTTP:Authorization},L]
#
########## End - Joomla! core SEF Section