In "User Overrides" there's a check box under "Advanced Settings": "Make minimize button minimize to the tray." This option tries to send apps to the tray instead of the taskbar, but doesn't work because anything that gets sent to the tray is being forced to the taskbar, even apps which normally don't need to be forced to the tray by an override.
Isn't anyone else having this problem? It's supremely annoying, especially with ZoneAlarm alerts, and I know a lot of people use ZoneAlarm.