Try again with JACK 0.99.48. It's in CVS now, but you probably need this tarball to get around the dreaded SourceForge anon CVS lag...
http://www.joq.us/jack/tarballs/jack-audio-connection-kit-0.99.48.tar.gz
The results I get with these versions are a lot more stable. But,
there are still some puzzles about the scheduling. Do you distinguish
different SCHED_ISO priorities?
JACK runs with three different SCHED_FIFO priorities:
(1) The main jackd audio thread uses the -P parameter. The JACK default is 10, but Rui's script sets it with -P60. I don't think the absolute value matters, but the value relative to the other JACK realtime threads probably does.
(2) The clients' process threads run at a priority one less (59).
(3) The watchdog timer thread runs at a priority 10 greater (70).
(4) LinuxThreads creates a manager thread in each process running one level higher than the highest user realtime thread priority.
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