Inaccessible virtual machines cannot be deleted occasionally in Virtualbox.
Fix it by issuing the below commands in a linux or Windows-DOS terminal.
To get a list of VMs run:
# vboxmanage list vms
The inaccessible ones will show up similar to:
# "<inaccessible>" {52a91e62-096d-4f8b-96f4-5fa76db3cd76}
Now use the GUID in the unregister command:
# vboxmanage unregistervm {52a91e62-096d-4f8b-96f4-5fa76db3cd76}
Problem solved.
A related article to this problem can be found here:
http://superuser.com/questions/468187/trying-to-open-a-vm-config-which-has-the-same-uuid-as-an-existing-virtual-machin