Not sure if the question below is Zimbra related, but I couldn't find anything in the Evolution bugtracker, so I give it a shot here 1st.
I use Evolution 2.8.1, coming standard with the Ubuntu 6.10 WS install. I have Zimbra 4.0.4 OS working on a clean Ubuntu 6.10 server version. I connect with IMAP and I get two trash and junk folders as can be seen in the first picture attached. What strikes me also is the different icons: 1 container seems to be a system folder, the other a regular map. Using e.g. Thunderbird, I don't get these double containers, see second attachment.