currently I'm using jackd version 0.116.1, before that I was using 0.109.2-3ubuntu1 (current intrepid version?), which already had this "issue".
I also noticed that different timeout settings made noticeable changes to this issue but it didn't solve the problem entirely, (btw. I already was using 9000ms, and this watchdog is not jack-related but built into pd / gui as far as i know.)
when trying different things concerning realtime permissions I also noticed that priorities for "audio" group in /etc/security/limits to something below 10 (don't know exactly anymore) also had an influence (because pd had no more rt permissions then).
now everything's fine when jack is started with sufficient priority, no matter which other settings I use with jack (except dropouts with too low latency or doing graphics stuff with gem in the same instance of pd).
Martin
Strange but I have no dropouts when running those patchs on my laptop with both alsa and firewire jack backends. So I give a try on 2 others hardware and no matter what I do dropouts are always here ...
I think your case was different since I have no crash like " zombified - calling shutdown handler " but "only" watchdog: signaling pd... and dropouts. And troubles arises only when the -rt patch is started with -nogui.
Very simple patch like just [osc~] and [dac~] doesnt' trigger the watchdog.
Joël