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I think no, jackd is not killed by pre-stop script.
Here's a log of a simple start and stop using the gui buttons:

13:20:14.724 Logging started --- mer mar 24 13:20:14 2010 ---
13:20:14.739 Patchbay activated.
13:20:14.762 Statistics reset.
13:20:14.808 D-BUS: Service not available (org.jackaudio.service aka jackdbus).
13:20:14.979 Startup script...
13:20:14.980 pulse-into-jack pre-start
13:20:14.983 ALSA connection graph change.
Executing "pre" action for pulse-into-jack
Killing and storing applications connected to PulseAudio
*** ***
skype
*** ***
13:20:15.781 Startup script terminated successfully.
13:20:15.782 JACK is starting...
13:20:15.782 /usr/bin/jackd -P70 -t5000 -dalsa -dhw:1 -r48000 -p128 -n2 -Xseq
13:20:15.784 JACK was started with PID=7456.
jackd 0.118.0
Copyright 2001-2009 Paul Davis, Stephane Letz, Jack O'Quinn, Torben Hohn and others.
jackd comes with ABSOLUTELY NO WARRANTY
This is free software, and you are welcome to redistribute it
under certain conditions; see the file COPYING for details
JACK compiled with System V SHM support.
loading driver ..
apparent rate = 48000
creating alsa driver ... hw:1|hw:1|128|2|48000|0|0|nomon|swmeter|-|32bit
control device hw:1
configuring for 48000Hz, period = 128 frames (2.7 ms), buffer = 2 periods
ALSA: final selected sample format for capture: 32bit integer little-endian
ALSA: use 2 periods for capture
ALSA: final selected sample format for playback: 32bit integer little-endian
ALSA: use 2 periods for playback
13:20:15.987 Server configuration saved to "/home/revol/.jackdrc".
13:20:15.993 Statistics reset.
13:20:16.031 Client activated.
13:20:16.032 Post-startup script...
13:20:16.033 pulse-into-jack post-start
Executing "post" action for pulse-into-jack
Restarting stored applications connected to PulseAudio
*** ***
skype
*** ***
13:20:16.455 Post-startup script terminated successfully.
13:20:16.457 JACK active patchbay scan...
13:20:16.458 ALSA active patchbay scan...
13:20:16.459 JACK connection change.
13:20:16.460 ALSA connection change.
13:20:16.661 JACK active patchbay scan...
13:20:16.662 ALSA active patchbay scan...
13:20:26.529 XRUN callback (1).
**** alsa_pcm: xrun of at least 31.983 msecs
13:20:27.921 XRUN callback (2).
**** alsa_pcm: xrun of at least 31.301 msecs
13:20:28.486 XRUN callback (1 skipped).
13:20:28.514 Client deactivated.
13:20:28.526 Shutdown script...
13:20:28.527 pulse-into-jack pre-stop
Executing "pre" action for pulse-into-jack
Killing and storing applications connected to PulseAudio
*** ***
skype
*** ***
13:20:29.310 Shutdown script terminated successfully.
13:20:29.310 JACK is stopping...
jack main caught signal 15
subgraph starting at PulseAudio JACK Sink timed out (subgraph_wait_fd=18, status = 0, state = Triggered, pollret = 0 revents = 0x0)
13:20:34.113 ALSA connection graph change.
13:20:34.131 ALSA active patchbay scan...
13:20:34.182 JACK was stopped successfully.
13:20:34.184 Post-shutdown script...
13:20:34.185 pulse-into-jack post-stop
Executing "post" action for pulse-into-jack
Restarting stored applications connected to PulseAudio
*** ***
skype
*** ***
13:20:34.596 Post-shutdown script terminated successfully.

Everything works well doing start/stop.

The problem is when I start and quit the app, behaviour that can be seen on my previous post.
What do you mean with "stub"? Something like "execute the scripts separately in a shell"?

Thank you

P.S.: this captcha is driving me crazy!! too difficult!!