HandBrakeBatch 1.5 works correctly on Lion, but there is a bug preventing the user to select an output folder visible on 10.6 Snow Leopard.
The bug has been fixed and the program should run correctly on Snow Leopard as well. If you are on Lion there is no harm in upgrading, and I have fixed another minor bug on the output folder selection dialog.
You can download version 1.6 here, or check for updates in the application itself.