I'm running the open source version (4.0) on a server, and I copy the zimbra directory each morning around 4 AM. I do so by stopping the server with zmcontrol, copying the zimbra directory to a different folder, and then starting the server.
When I ran previous versions, I never had a problem with this, but after upgrading to version 4 I end up with all of the email that was received after the backup being queued. Running zmcontrol status shows that antispam and antivirus are not running, but simply restarting the server does not get them running again. I have to stop the server, run /opt/zimbra/libexec/zmfixperms, and start the server again to get it running.
The only reason that I figured out that zmfixperms would get the server to start again was that I was trying to get the wiki to work in 4.0, and one of the forum posts that I read said you had to change some permissions to get it working. I did that, and the next day when the problem above occurred, I just assumed that I needed to run zmfixperms because I messed up some permissions. Unfortunately, it's continued to occur each day, and I haven't been able to find any information relating to it.
Here is my nightly backup script:
Any insight on this would be greatly appreciated. Thanks!
su - zimbra -c "zmcontrol stop"
cp -r /opt/zimbra /home/backup/backups
chown -Rf backup /home/backup/backups/opt-zimbra
su - zimbra -c "zmcontrol start"