When using OSS Zimbra 3.0.1 with IMAP clients and not just the web interface, we're seeing a lot of cases where the new message count within the Zimbra web interface is incorrect.
For example, one user of ours used squirrelmail to delete 3 messages the other day (his parents have dialup ;-) When he went to the Zimbra web interface, the Trash folder showed that there were 3 new messages, but really, no messages at all were in that folder (new or old). Choosing 'Empty Trash' does not solve the problem.
For me, I mainly use mutt, which uses Zimbra as an imap server. Looking in mutt now, there are no new messages. Going to the Zimbra web interface, it says that there's 60 or so new messages, but there actually aren't any new ones.
When I use the phrase "It think's there are X new messages", I'm referring to the message count in parenthesis after the folder name, in the folder list on the left.
My appologies if this was an issue already solved in 3.1.0. I have not yet upgraded, as I was hoping to wait a few days for the installer kinks to get worked out, these guys would get irate if they went without email for more than a few minutes ;-)
I didn't see it mentioned in bugzilla, the release notes, or the forum, so I figured I'd take the chance that this issue was present in 3.1.0 as well :-) If you prefer I upgrade first, I can get back to you in a few days as to whether we're still seeing this.