Yes, this is a problem I have as well. Running PD with ALSA, I get reliable playback, but running with JACK in realtime I get clicks, even though every other program (Ardour, Specimen, etc) work fine. I suspect it's PD Jack interface.
Speaking of which, I have to run PD using the -alsa switch and then switch over to the JACK interface (Media->JACK) in order for PD to connect to the JACK server. I've heard of at least one other person who had this problem, who was kind enough to let me know the solution (selecting another interface first).
Thanks for the replies so far, I'm interested in anyone else's experiences with JACK and PD.