nothing is going to work if your BES agent doesn't come up.
the zimbra portion of things kick in only after the BES agent is running so you are debugging a BES specific issue. are all of your blackberry services running?
i know that there is a timing issue with the sql service and other BES services which may be your problem. if you open up your services control panel applet and there are some blackberry services which are "automatic" but are not started, you may be experiencing these timing issues. try manually starting these services and then restart the controller.