I thought I'd try a fresh install to see if the problem still existed. So far I have no issues following a few test restarts of the system.
I think it may possibly be linked in to using Likewise-Open to join the Ubuntu VM to a Windows domain as first install things went wrong after installing likewise-open5 and joining the domain. Second install I joined the domain first then installed Alfresco and it went faulty after the first reboot. Less likely but still possible, adding extra users to MySQL may have caused it as I added another account to allow me to connect remotely with MySQL Administrator. I will test these to see if the issue comes back again.