After looking at various file in the /etc/pam.d directory, I also tried adding the 
session    required   pam_limits.so
line into the 
- /etc/pam.d/common-session
- /etc/pam.d/tigervnc file

... with no visible effect.

And between each attempt I actually rebooted the machine, so it's definitely getting it's chance.

So the current status is that
 - if I log in via ssh from my iMac, the ulimit -r result is what we want
 - if I try from a terminal running via the VNC desktop, it is not what we want.
 - if Squeak is run within a systemd file, it works by virtue of the LimitRTPRIO=2 command

The system is x64 xubuntu with tigerVNC added. It may be of note that tigerVNC is running from a systemd file and that it seems to stop occasionally and require a manual restart. 

tim
--
tim Rowledge; tim at rowledge.org; http://www.rowledge.org/tim
Useful random insult:- Full of wisdumb.