Well, this may have helped to explain why command-line shutdown doesn't work, as well.
/proc/stb/fp/wakeup_time is the next wake-up time. and this seems to be left at 0 when the box is running.
There is a Python function - setFPWakeuptime (from Tools.StbHardware) - to write the (Epoch) time of the next wakeup to this. So presumably(?) something uses this to set the next time to wakeup as part of the shut-down process.
[Perhaps there's some reason not to have this always populated with the next event time - such as odd things happening if the front-panel tried to start the system when it's already running?]
So, if I really want a command line shutdown then I just need to grab the setting code which is in mytest.py in the OpenVIX enigma2 git repository and run that before shutdown (or even add it is a generic shutdown script if the current wakeup_time is 0).