I did an upgrade from 5.0.23 to 6.0.7 yesterday on an Ubuntu 8.04 installation. The install is using vhosts for redirection to a couple of virtual machines, and the zimbra install is on port 81 per the documentation.
During upgrade, I got a notification that zimbra-store had a port conflict with 80, although the install settings had the http port correctly set for 81. So, I turned off apache so the server could get up in running, then restarted it when the install completed.
Since I am using the community version, I have the server go down nightly for backups, and it is now not restarting properly.
What is the method for moving zimbra-store back to the correct port 81?