Same issue here. I have Zimbra Desktop minimized to my system tray, have "popup notifications" enabled for both mail and appointments, but only see the Zimbra red systray icon turn into an envelope.
Note - I have the Zimbra Web Client on Firefox open as well (I do all my work in the web client, but have installed Zimbra Desktop for the sole purpose of providing me with popup notifications). Any clues?
P.S. It would be great if Toaster handled appointment notifications as well - this way I don't have to install the giant Zimbra Desktop software just to get notifications.
You could use Zimbra Notifier, which notifies you of new mail and new calendar events.
It's in Zimbra Gallery, in "extras" category.