Having this issue as well.
We have multiple files added per week, all with the date in the filename:
Awesome File 14-06-03
Awesome File 14-06-02
Awesome File 14-06-01
We have WP-Filebase default order set to display by title, Descending.
Since the update they are listed Ascending like so:
Awesome File 12-10-09
Awesome File 12-10-10
Awesome File 12-10-11
...
Awesome File 14-06-01
Awesome File 14-06-02
Awesome File 14-06-03
Changing the default sort order and/or Ascending/Descending does nothing.
It is crucial that this works as we have people paying for these files so they need to be displayed in the correct order.