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yes the path was a problem, i just specified it in the configuration script, still no go. Here is what i get:

11:52:23.379 Patchbay deactivated.
11:52:23.380 Statistics reset.
11:52:23.394 ALSA connection graph change.
11:52:23.591 ALSA connection change.
11:52:26.827 Startup script...
11:52:26.827 artsshell -q terminate
11:52:27.281 Startup script terminated with exit status=256.
11:52:27.282 JACK is starting...
11:52:27.282 /usr/bin/jackd -v -R -dalsa -dhw:0,0 -r48000 -p256 -n2
Unknown option character
jackd 0.116.1
Copyright 2001-2005 Paul Davis 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
usage: jackd [ --realtime OR -R [ --realtime-priority OR -P priority ] ]
[ --name OR -n server-name ]
[ --no-mlock OR -m ]
[ --unlock OR -u ]
[ --timeout OR -t client-timeout-in-msecs ]
[ --port-max OR -p maximum-number-of-ports]
[ --debug-timer OR -D ]
[ --verbose OR -v ]
[ --clocksource OR -c [ c(ycle) | h(pet) | s(ystem) ]
[ --replace-registry OR -r ]
[ --silent OR -s ]
[ --version OR -V ]
[ --nozombies OR -Z ]
-d backend [ ... backend args ... ]
The backend can be `alsa', `coreaudio', `dummy',
`freebob', `oss', `sun', or `portaudio'.
11:52:27.292 JACK was started with PID=4236.
jackd -d backend --help
to display options for each backend
11:52:27.295 JACK was stopped with exit status=255.
11:52:27.296 Post-shutdown script...
11:52:27.296 killall jackd
jackd: no process killed
11:52:27.703 Post-shutdown script terminated with exit status=256.
11:52:29.404 Could not connect to JACK server as client. - Overall operation failed. - Unable to connect to server. Please check the messages window for more info.

Now when i copy and paste : /usr/bin/jackd -v -R -dalsa -dhw:0,0 -r48000 -p256 -n2
in a terminal i have no problems, but when i try to fire it up in qjackctl no go with or without realtime priority. Seems a bit odd. Maybe you can help me on this one. And as for realtime limits i managed to solve that problem with PAM (i had to patch PAM and recompile and reinstall it and the shadow package as well) or set_rlimits.
in case you are interested this is the PAM patch:

--- modules/pam_limits/pam_limits.c.orig 2005-07-06 09:05:32.000000000 +0100
+++ modules/pam_limits/pam_limits.c 2006-03-05 12:37:56.000000000 +0000
@@ -30,6 +30,7 @@
#include <sys/types.h>
#include <sys/stat.h>
#include <sys/resource.h>
+#include <asm/resource.h>
#include <limits.h>

#include <utmp.h>

and also /etc/security/limits.conf must be edited as well
Anyway if you have any ideas on this one please let me know.