Hi there,
I have a similar problem. Zimbra 6.0.6 is installed on my server at home. My primary account has an email address on the local network (loc.empec.de). There are several external accounts (ie for domain empec.de). When I send an email using one of the external accounts as sender, my local email address still appears in the Return-path-Header. Many of my emails are directly going to the recepients spam folder. Other people do report, that they don't get emails from me 
This looks like this (excerpt):
Return-Path: <michael@loc.empec.de>
From: <external_account_name@empec.de>
Subject: Header
MIME-Version: 1.0
Content-Type: text/plain; charset=utf-8
Content-Transfer-Encoding: 7bit
X-Originating-IP: [192.168.10.102]
X-Mailer: Zimbra 6.0.6_GA_2332.RHEL4 (ZimbraWebClient - FF3.0 (Win)/6.0.6_GA_2324.UBUNTU8)
Any idea how to change this so the used sender email address is used?
Thanks a lot
Michael