403 Forbidden Error when using Pro Sites

I am getting a 403 Forbidden Error when I click on the Submit button on the Settings TAB of Pro Sites.
I am running a subdomain multisite - which has a wildcard A record setup and dedicated IP Address. The install is also in the root directory.
I have disabled pretty much every plugin except for the WPMU Dev Dashboard.
I have been able to map a domain name to the multisite (WHMCS, Domain Mapping, MU Provisioning) - that all worked however I cannot make any setting changes in Pro SItes. And occassionally I cannot log into the Admin Dashboard (403 Forbidden error)?

Here is the htaccess file :

# BEGIN WordPress
<IfModule mod_rewrite.c>
RewriteEngine On
RewriteBase /
RewriteRule ^index.php$ - [L]

# add a trailing slash to /wp-admin
RewriteRule ^wp-admin$ wp-admin/ [R=301,L]

RewriteCond %{REQUEST_FILENAME} -f [OR]
RewriteCond %{REQUEST_FILENAME} -d
RewriteRule ^ - [L]
RewriteRule ^(wp-(content|admin|includes).*) $1 [L]
RewriteRule ^(.*.php)$ $1 [L]
RewriteRule . index.php [L]

# END WordPress