This is just a guess, but:

There might have been a typo in your original hand-made list of favorite visuals, or some other kind of error in your config file, and this is breaking the new Emplode's visual-management system.

Try deleting all the favorite visuals through the new "Favorite Visuals" item on the Tools menu and see if that makes the problem go away. If not, try editing the config.ini file directly.

Note: I had trouble being able to edit my config.ini file through emplode after beta11, not sure why and I'm not sure whether it's an actual bug or not.