The Pro Tools software has been deployed to all of the Macs in Milne, for better or for worse, and most of the machines have been rebooted.
And the shutdown/restart/ and now logout problem is alive and kicking. I have tested several machines in Milne and they have all exhibited issues shutting down. I was incorrect earlier.
The dock doesn’t disappear, just the Apple Menu, but the shutdown problem still happens exactly as described earlier.
Fortunately, we only have to live with this until the end of the Winter term 2016, and then we’ll be able to take Pro Tools off of the machines, hopefully for good.