I found that I needed the shutdown command to be run as root.

Also added a note about shutdown_command that bit me.

website/source/docs/builders/virtualbox.html.markdown

@@ -28,11 +28,16 @@ Ubuntu to self-install. Still, the example serves to show the basic configuratio
   "iso_checksum": "2cbe868812a871242cdcdd8f2fd6feb9",
   "iso_checksum_type": "md5",
   "ssh_username": "packer",
+  "ssh_password": "packer",
   "ssh_wait_timeout": "30s",
-  "shutdown_command": "shutdown -P now"
+  "shutdown_command": "echo 'packer' | sudo -S shutdown -P now"
 }
 </pre>
 
+It is important to add a `shutdown_command`. By default Packer halts the 
+virtual machine and the file system may not be sync'd. Thus, changes made in a 
+provisioner might not be saved.
+
 ## Configuration Reference
 
 There are many configuration options available for the VirtualBox builder.