This is more a warning of a new issue in Vault 2013.
Situation: you want to create a new Vault with an existing config file and a cusotmized File Location (Filestore):
Result is that the new Vault is created with the Config File but the File Location is still the default one:
Solution is to move the Filestore after the creation of the Vault to the expected location via RMB on the Vault "Move File Store":