If you install Web Deploy 3.x BEFORE Web Management Tools are installed, you’ll have to re-install Web Deploy. I beat my head against the wall for hours on this.
- Install the Web Management Services (“Turn Windows Features On/Off”/Roles -> Web Server -> Management Tools -> Management Service)

- Then uninstall Web Deploy (repair didn’t work) via the usual Add/Remove Programs control panel

- Install Web Deploy 3.x again using Web Platform Installer.
Fixed. /Sigh