OK, I think we're good!

I added jack to the auto start list, and set it to start in the system tray so it doesn't clutter my Task Manager.

For anyone else reading this, Jack will get confused if you have your open applications (session) saved and loaded on shutdown and startup as well - You'll have jack restored from last session and jack from auto start. They may both run , they may not. If you quit one, the other gets disconnected too.

So either

- don't save your sessions,
- add jack to the list of apps to be excluded from saved sessions
- don't put jack in your auto start.

If jack still throws up errors on startup, you might want to increase the 'Start Delay (Secs)' in the options to give it time to do all the things it needs to while the computer is also doing whatever else it does on startup.

Getting jack and pulseaudio to work together using jack sink took a couple of restarts but was pretty easy.

So now I can finally use Amarok at the same time as Muse, Hydrogen, ZynAddSubFX etc. and all without any manual configuration at boot.

Let the music creation commence...