I seem to be having a similar problem with my installation. I can add new categories but I can't delete anything. When I try, I get this message: "Success 0 categories successfully trashed". I can add new categories but can't delete. I can delete the records in the database table the hard way though using phpMyAdmin though my hosting company's console.
This is on an install done today so when I checked the above noted file and code I see that it is present so I do have the updated version that is talked about above.