i found out the problem happens early. I recorded on the RPi a source that is known to be click-less into a file (with edirol ua1-ex) and then analyze the file. the file seems to have the clicks, that always look similar in the spectrum.
here is some output of the system:
pi@raspberrypi ~ $ cat /sys/devices/system/cpu/cpu0/cpufreq/scaling_governor
pi@raspberrypi ~ $ df -h | grep shm
tmpfs 128M 24M 105M 19% /run/shm
pi@raspberrypi ~ $ cat /proc/asound/cards
0 [UA1EX ]: USB-Audio - UA-1EX
EDIROL UA-1EX at usb-bcm2708_usb-1.3, full speed
pi@raspberrypi ~ $ jackd -p16 -t2000 -dalsa -dhw:0 -p1024 -n3 -r44100 -C
Copyright 2001-2005 Paul Davis and others.
Copyright 2004-2012 Grame.
jackdmp 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 server starting in realtime mode with priority 10
creating alsa driver ... -|hw:0|1024|3|44100|0|0|nomon|swmeter|-|32bit
control device hw:0
configuring for 44100Hz, period = 1024 frames (23.2 ms), buffer = 3 periods
ALSA: final selected sample format for capture: 16bit little-endian
ALSA: use 3 periods for capture
pi@raspberrypi ~ $ jack_rec -f /run/shm/a_jack_rec.raw -d 10 -b 16 "system:capture_1" "system:capture_2"
disk thread finished
analyze file with baudline, results here
(to check, the clicks can be heard for instance at around 950 ms and 1400 ms in this 10 sec sample)
i wonder why there can be clicks if no x-runs are reported and no resampling is involved. is this an issue of jack or of the audiointerface maybe? i used the ua1-ex on another machine (not via jack) but without similar issues. i am a bit stuck now..
thanks for the help,