Hi..I think the ISSUE you talking about is not an ISSUE but a function of account type "zimbra"..when you were asked to setup a new account you choose "Zimbra" instead of "IMAP" option from the dropdown.
if you choose "Zimbra" account type you get full mirror of the zimbra account synced on your computer so you can take use of offline/online mode of zimbra and all its collaboration functions..
if you simply choose "IMAP" as new account type you will get exactly what you need, try and let us know what you think.
* you can read about "account setup" and other things here
Zimbra Desktop - Zimbra :: Wiki
Raj