Did you get this sorted?
Every time I reboot I lose my VM's. On one of my unraid servers the VM info in Virtualbox is saved and survives reboot but the other does not. I just don't know why it saves on some and not others.
Sounds like you need to change the default location of your Vitualbox VM's. If you are using phpVirtualBox you can change this location from the "File --> Preferences" and change the "Default Machine Folder" location. For instance, mine is set to "/mnt/user/Apps/VirtualBox VMs".