There should be an audio file labled director's comentary. Which you will need to untick the box. It could also be labled unknown.
Director comments and special features etc. are generally the 2 channel audio feeds...I remove all audio except AC3 5.1, this will generally downmix to 2 channel for viewing without surround sound.
When only choosing AC3 5.1, you will have no other audio on the backup besides the dialog and soundtrack.