I've been having this problem for quite a while... whenever I quit PD, jackd crashes after a few seconds. Looking in the Connections window in qjackctl, I can see that PD's ports remain after quitting until the crash. If I run jackd in the terminal with the same command as qjackctl runs (jackd -R -P89 -t10000 -dalsa -dhw:0 -r44100 -p128 -n2 -P -S) , its last words are:
jackd watchdog: timeout - killing jackd
I'm running Debian testing, jackd 0.101.1-1, Pd-0.39.2-extended-test4, but this has been happening for several PD versions (not sure when it started). Is anyone else seeing this? One other jack app I know of, jack-rack, actually has the same problem.
Ben