Thanks. I will blame it being 3am for me being so dumb, don't actually know why it changed/got corrupted on Mysql though.
I will try and post my migration experience when finished as 3.x migration information on CentOS seems rarer. I chose to do it this way as I needed to upgrade php to support Wordpress 3.2.1 or higher so I felt the safest way to migrate the host was to move to a new VM running the new CentOS.
Now to make sure email is all working, but all the websites which was the only important bit are fine and I have also now upgraded to the latest ISPConfig too.