Just to confirm: yes, this feature worked in ZCS 5.x, but the upgrade to ZCS 6.x broke it. It is not fixed as of 6.0.1. Apparently, the bug was present in earlier versions of the Zimbra desktop and has migrated into ZCS as of the 6.0 release.
My users are trying to access external POP accounts from Hotmail/Windows Live Mail and are running into this bug. Unfortunately, they very much need to leave messages on the server.
Please be sure to vote for
Bug #30643 and
Bug #41213 to let the Zimbra team know this bug is important to resolve.