For the zip issues, try this:
1. Log on to Messaging
2. Click on Start -> All Programs -> Microsoft ForeFront Server Security -> FSE Administration
3. In FSE Admin, click on Settings -> General Options
4. Deselect “treat zip archives containing highly compressed….”
You can check under Report -> Quarantine as well to verify that this is the rule that was affecting your mails.
Thanks to Mark for this hint.