This is happening on all MKV files not specific files, so I would assume this is a software/settings error rather then something to do with the file itself? It also does not happen at the same part twice, I cannot really make it happen, it just tends to happen randomly. sometimes I can make it happe...
When you click the speaker in your toolbar, click mixer at the bottom and make sure the individual VLC volume under "applications" is maxed and not down.