Update to Apple Configurator 1.2.1 or later via the Mac App Store's Updates tab.
In most cases the migration should complete in less than a minute. However, it may take longer if you have manually added iOS installation (.ipsw) files to Apple Configurator (by choosing the "Other..." option in the iOS popup menu from the Prepare pane). Those files were stored outside of the Apple Configurator database in Apple Configurator 1.1.2 and earlier versions. Starting with Apple Configurator 1.2, all .ipsw files are copied into the database to ensure file availability for device installations. If the files are on a remote server volume or if you have multiple iOS releases for multiple device types, the database migration could take thirty minutes or more.
Wait for Apple Configurator to complete the migration process, even if the application appears to not be responding. This is a one-time migration and should complete when all the .ipsw files have been copied into the new database.