The following article not only details an alternative backup method to vaults (Time Machine), but also provides a number of steps that may be helpful in getting Aperture working as expected again.
Back up your library
Before troubleshooting Aperture, it's a good idea to create a backup of your library if you don't already have one. You can use Time Machine, or create a Vault in Aperture to make your backup. Note that Time Machine does not fully back up the Aperture library when Aperture is running, so be sure to quit Aperture and allow Time Machine to perform a complete backup before proceeding.