Hi @tim,
this is because:
“Basically once you start Jack Pulse won’t be available because Alsa/Jack have occupied you soundcard (that is why, if you want to listen to some mp3 files during such a session e. g. you will have to use a Jack-capable music player like audacious).” (see: Jackd/ALSA (Linux) best practices for SP?)
You can run Pulse audio through Jack to solve the problem - though up to now I have not yet found a reliable configuration (but that is probably me being to stupid 
).