The audio shift option only works for the first track, all other tracks will not be changed.
And it doesn't seem to be the first time someone has mentioned it.
Audio output - shift applies only to the 1 track (https://avidemux.org/smif/index.php?topic=19094.0)
Via Audio menu/Audio Tracks click the "Apply settings to all tracks" button. When you return to the main window you will see number of tracks in brackets next to Audio Output.