hi,
the realtime kernel of ubuntu jaunty is buggy!
i've compiled a new rt-kernel and everything is working well (no glitch, no drop-out even with a very low latency (64 frames/periods)). you need a good realtime kernel, ubuntu studio was working on releasing a new rt-kernel for 9.04. i don't know if it's already available in launchpad...
also, you can try to run jackd & pd in root. this way you will know if it's a wrong setup in limits.conf or such.
and read this: http://wiki.linuxmusicians.com/doku.php
pat