OK, I tried this method from the command line on my Ubuntu 6.06 LTS install, and when I used the
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su - zimbra -c "zmcontrol start"
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method, although zmcontrol status showed all the modules running, the web UI shows red "X" by Spell, SNMP, MTA, and Antivirus as well as Status. Just going from root to su - zimbra and then running zmcontrol stop & start, and the only red X is by Status. I don't know why, or even where to look to find out why, but if I had to guess I wonder whether running the whole command from root results in some odd file permissions issues.
I'll be interested to hear how it works (or not) for SSS. . .by the way, you didn't say what version you were on. I presume "yum" means SuSe, but what release of Zimbra?
Whatever is going on, although I've had that red X by Status for a couple of weeks (despite stopping & restarting using the shell script backup every night), I am unable to tell that it hurts anything. The graphs and the nightly summary emails are clearly generated by other processes.
Dan