Joomla SEF Apache mod_rewrite not working on new hosting setup, possible RewriteBase rule?

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I recently moved my sub-domain hosted Joomla (sub.domain.com) to another host and my SEF URL's are broken. Currently I have Apache mod_rewrite turned off in the Joomla admin forcing the /index.php/ within all URL's

Apache mod_rewrite is loaded and working correctly. The major different in my hosting setup is that before my VPS host had a directory for the sub-domain within the server structure /home/me/sub.domain.com/ now it seems the new host is using another rewrite? as the server files is located in /var/www/domain.com whereas the front-end browser points to http://sub.domain.com

Not sure if there is a custom RewriteBase rule I'm not familiar with to correct this or perhaps there is another rewrite going on within the hosting which I'm not aware of?

Thanks for you time.

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Have you made sure, that you DO NOT have set AllowOverride in your vhosts file to "none" ?