I did a mostly-successful upgrade from 5.0.8 to 5.0.11 on Ubuntu 6.06 LTS last night, but noticed two hiccups when I restarted the server at the end of it all. One, logger and SNMP showed not started on the status window, and two, when I went to zmcontrol status, in addition to these two services, ClamAV was down with the usual "Don't Panic!" message for outdated databases. Not exactly sure why these were outdated the moment of installing a new version, but c'est la vie. . .
Anyhow, repaired the Clam problem using the ClamAV - Reset Defs DB - Zimbra :: Wiki wiki article, and when I re-started the whole Zimbra package everything (including logger and SNMP) came up swimmingly.
If this experience mirrors anybody else's, we may need to file a bug. On the other hand, if it's just me we'll chalk it up to my good luck. . .