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
I digg a litlle further and found out it's probably a scheduling issue. When the gui send the "I am happy" signal to the watchdog process all is fine but when there is no gui this task is devoted to the main process and sometimes fails to do it in time. As a very ugly workaround I comment out the kill(getppid(), SIGHUP); line in s_watchdog.c Watchdog is still signaling as before but dropouts are gone! To be sure the pd patch outputs a 1Khz sinewave monitored with jaaa in peak hold mode.
That's all my little knowlegde can do...
All the best Joël