I found a thread with details about resetting the mysql password: http://www.zimbra.com/forums/showthr...tialize+logger and that seems to have fixed the problem. Tried rebooting a couple of times and stoping and starting zmcontrol. Haven't managed to break it yet. Happy days. Thanks MarcMac for all your efforts.
Glad to hear you found the problem - as you surmised, tomcat gets config data from mysql, so it won't start if it can't get said config data.
The thing that seems strange to me is that it was only java that was complaining about it. When I did a mysqladmin status it seemed to be ok. Is it not possible to modify one of the scripts to show the error when you start it? I thought about posting to bugzilla but I'm not really sure what caused the problem.