I am having this issue since quite a while ago and I cannot find an answer.
My system is Debian Stretch, currentry using qjackctl (jack package is jackd version 5, depending on jackd2, which is installed). Since I use other apps that require this version of jack, it's not an option to change to jackd1). The symptom is that pd-gui refuses to close upon exiting. I have to send a sigterm message via htop to make it close.
Any hints on how to solve this will be appreciated.