Thanks for the suggestion. I couldn't find any reference to chroot anywhere in any of the conf files.
I ended up finding the problem, I used to have plesk installed on this box (Wasn't my choice, people we are renting it off of.) I have now removed it but it seems a lot of the old config files are still lurking around the system, more specfically one called "zz010.psa.httpd.conf" which, holds the solution to my problem! As it holds the config for the default site! Added in the /etc/MailScanner as an allowed path, made the other necessary changes and now have it working.
Thank you for the suggestion.