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In a specific file, when moving from one chapter to another, the audio becomes very choppy. This occurs in the latest stable VLC (2.1.5.) as well as in the latest nightlies. It does not occur in mpv. I don't currently have access to Windows to test if this affects VLC on that OS as well, sorry. This does not occur in a number of other mkv files I tested, and seems to be something specific about this one. Seeking to a point sufficiently past the chapter transitions causes the audio to work correctly. Checking Console shows several instances of the following message when this is happening:

"10/9/14 4:45:30.406 AM VLC[62449]: Can't find app with identifier com.spotify.client"

I don't have Spotify installed, so I suppose it indeed wouldn't find it, to do whatever it is it's looking to do for some reason.

Link to mkv file in question: http://crl2qw4pym.1fichier.com/

I can replicate this consistently by pressing the "next chapter" hotkey. Whatever other information might be requested will be provided as best I'm able to

Don't mean to double post, but there doesn't seem to be an edit button or I'm just entirely failing to notice it.

After checking around, the problem with the audio seems to be related to how VLC handles playing back aac/adts files with mixed channel configurations or sampling rates. I've also been able to verify with other people, including Windows users, that they experience the same thing when attempting to play that file in VLC.

Please file a bug report at https://trac.videolan.org/vlc/, together with VLC version, sample file and log output.