For what I can see on the hosted demo and on my own installation, Zimbra uses the same approach of Microsoft Outlook to create "conversations" (message threading), which is to based a relationship on the subject line. That is very inaccurate, extremely. People who might use the same subject over and over --on completely different emails, different conversations-- will see their messages "tangled" with others.
Please, use message-id, in-reply-to and reference for threading. In other words, please, please, make threading strict.