IIRC, Ubuntu "RT" kernel is not actually Real Time (i.e. with Ingo patches), just a "desktop RT" which is not very useful for audio and certainly not enough for JACK apps of any heft.

Where are you getting this info from?  This is not what I have read, but maybe I am missing something somewhere.  I thought that the Ubuntu kernel packagers recently switched to using full realtime preemption... I find this in the package description of linux-image-2.6.22-14-rt :
Ingo Molnar's full real time preemption patch (2.6.22.1-rt9)

Here is the output of uname -a:
Linux pal 2.6.22-14-rt #1 SMP PREEMPT RT Tue Feb 12 09:57:10 UTC 2008 i686 GNU/Linux

.. and here are the kernel settings from  cat /boot/config-2.6.22-14-rt | grep PREEMPT
# CONFIG_PREEMPT_NONE is not set
# CONFIG_PREEMPT_VOLUNTARY is not set
# CONFIG_PREEMPT_DESKTOP is not set
CONFIG_PREEMPT_RT=y
CONFIG_PREEMPT=y
CONFIG_PREEMPT_SOFTIRQS=y
CONFIG_PREEMPT_HARDIRQS=y
CONFIG_PREEMPT_BKL=y
CONFIG_PREEMPT_RCU=y
# CONFIG_DEBUG_PREEMPT is not set
# CONFIG_CRITICAL_PREEMPT_TIMING is not set

Looks realtime to me.. also the latency is really low (5-10ms conservatively), much lower than I have experienced on other OS's, with or without realtime.  But, if you know something I don't... I have open ears.  Ubuntu runs so nicely on a laptop though... would hate to switch after finding such an easy-to-operate linux distribution because pd and only pd doesn't like jack in realtime.

regards,
rich


The "pops/clicks" phenomenon you are noticing that gets resolved by starting or killing another JACK app, is something I've experienced before. It happens when some app gets an Xrun or otherwise can't process audio in time. From that point forward it "clicks" and, in my experience, distorts as well with some bitcrushing-style aliasing distortion. When you start or stop any JACK app, the entire JACK graph structure gets re-ordered (this isn't true with jackdmp, just with single-processor JACK), and that causes the misbehaving app to "start from scratch" somewhat and get its audio organized properly.

I'd suggest 64Studio, Musix, Pure::Dyne, or some other distro that has the really serious RT set up with the Ingo patches. With one of those distros, everything should run very well on a machine of any decent heft.

-ken