When the input features multiple audio tracks, then the dropdown for users to choose audio output format, fails to affect the rest of the tracks. This tends to trigger no less than THREE DIFFERENT ANNOYING PROMPTS on save.
Please use the audio tracks dialog ("Audio" --> "Select Track") to handle up to 4 tracks. The combobox in the main window is designed to affect only the first track, else it would easily destroy the setup configured in the audio tracks dialog. Specific requirements and limitations of some audio encoders make an "apply to all tracks" checkbox not viable.