This problem went away at some point, though I can't necessarily pinpoint when it happened. Possibly in a minor version upgrade, possibly when we went to 6.x. It is definitely working, though, as I just received a message addressed to the whole school in the last couple of days.
A somewhat-unrelated issue we encountered with students was that many of our students forward their messages to an external, personal account, and that messages delivered to a nested distro wouldn't forward. The message would land in their Inbox, but not get forwarded on. This did not happen when the message was sent to the
classof2013@school.org address, however; in these cases the messages were forwarded normally. This also seems to have been resolved, though.
All things considered, we've been extremely happy with our Zimbra installation, and would recommend it. The web client is robust, server setup is a relative breeze (in testing, we went from download to installed, functional server [including LDAP integration] in < 3 hours), and with ActiveSync masquerading, our smart phone users are happy. There are some minor issues I've had in the past with UI, but even those have apparently been resolved in version 7, to which we'll be migrating this summer.
Feel free to e-mail with any specific questions.