Try using the VBoxManage command:

VBoxManage list runningvms 

should give you the name of the VM you want to shut down

VBoxManage controlvm VMNAME poweroff 

powers off the VM.

Try using the VBoxManage command:

VBoxManage list runningvms 

Which gives you the name of the VM you want to shut down. For example:

"rails_1366055054" {8144df4b-941f-40d6-ba5f-6e83d398ffd3} 

To shut down this VM, you run

VBoxManage controlvm "rails_1366055054" poweroff 

Note that this advice only applies when using the VirtualBox provider.