When you started Alfresco manually, did you start it as root? Alfresco is quite sensitive to file permissions, particularly in the alf_data directory, so starting Alfresco as the same user every single time is pretty important. It's easy to inadvertently change users when you configure Alfresco to start automatically.
The port remappings are needed because some of the protocols Alfresco serves (CIFS, FTP, NFS and SMTP) use privileged ports, so on *nix systems Alfresco either has to be running as root or else those ports need to be remapped to non-privileged ports with iptables or the like used to forward the privileged ports as needed (some of the clients for these protocols cannot be configured to use alternative ports eg. the CIFS client built into Windows, hence the need for port forwarding).
Another potential hiccup is that currently Alfresco has a small number of known issues on JDK 1.6, and I believe that's the version that's bundled with recent releases of Ubuntu by default. The problem you're seeing here is not related to JDK versions, but it's something to keep in mind going forward.