JACK input/output are not persistent
http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=579938
The JACK input and output instantiated by VLC come and go, as VLC opens the input item, or starts/stops the audio output pipeline. This does not work very well with the JACK model.
To work around this, I guess VLC would need a persistent interface plugin (or akin) that spawns the JACK connection and keeps it regardless of the VLC playlist state.