Hello.
Just installed a brand new Debian 9.
Running Jack from debian's package - 1.9.10+20150825git1ed50c92~dfsg-5
Star Jack with Qjackctl.
I get Xruns, or to be clear i get 1 xrun by hour (!)
The same if i leave the computer on, and leave it without any sound
application open/running, or browser or whatever. Just booted, start
jack/qjackctl & wait...
Same as I did when I tried Debian recently. Which desktop
environment do you have set up? One good rule of thumb is to use
LXDE, and to disable (or remove, if you can without breaking the
package structure) all GVFS items.