its happening to me too.
i recently upddated my version from the vlc-2.0.8 to the 2.1.5 because i always had an issue with trueHD audio chanel, the issue was some kind of pitching on the chanel for the music, and didn't affect the voice chanel, then i updated to 2.2.0 and the issue dissapear finaly after so many trie i could enjoy my good mkv.....but, and there is a but, now it seem any mkv will have a blank of 1 second just like if someone pushed the MUTE button around 14 second in the file, the same thing happened with the 2.1.5 but around 9 sec and only for audio file.
it now seem to affect any file that get play in VLC, and they were good on 2.0.8, nothing is using the CPU, nothing running in the background, glad to see i am not the only one.
i just reinstall 2.0.8 and fix everything, i have the bad pitch with the trueHD audio again but thats a good temporary fix, since it take less than 10 second to reinstall the 2.2.0 you can do that until someone fix the issue
nope now i got the problem in the 2.0.8 too, but its different it skip a second around 0:08 everytime i start an audio file, if dont start it back but rewind to the start it play ok, if i start it again it does the skip, this is really weird, i will try unninstall vlc completely and retry 2.0.8