May you try with your pre-shutdown script in stub mode, that is doing nothing but printing its invocation mode ?
I suspect you're bringing the jackd server down with pulseaudio, while on the pre-stop case and that just sounds like a race condition is lurking in there, as qjackctl will try to terminate jackd once again, right after the pre-shutdown script returns.
May you try with your pre-shutdown script in stub mode, that is doing nothing but printing its invocation mode ?
I suspect you're bringing the jackd server down with pulseaudio, while on the pre-stop case and that just sounds like a race condition is lurking in there, as qjackctl will try to terminate jackd once again, right after the pre-shutdown script returns.
Seeya