The mame cores I have installed are:
a) lr-mame2000
b) lr-mame2003
c) lr-mame2010
d) advmame
e) mame4all

Most of the arcade game mappings in the emulators.cfg file point to either lr-mame2003 or lr-mame2010.

The contents of the retroarch.cfg file in /opt/retropie/configs/mame-libretro/ is as follows:

input_overlay = "/opt/retropie/configs/all/retroarch/overlay/MAME-Horizontal.cfg" input_overlay_opacity = "1.000000" input_remapping_directory = "/opt/retropie/configs/mame-libretro/" # include "/opt/retropie/configs/all/retroarch.cfg"

So I don't see anything here that should override the global controller settings.

The runcommand.cfg file located on /opt/retropie/configs/all/ does not contain any code for the "launch menu joystick control" function right now - it does have:

disable_joystick = "0" disable_menu = "0"

...plus three other lines of code for use_art, governor, and image_delay.

I have tested the controller on the following console menus (accessed via the retropie configuration menu, from the screen where you would otherwise select a console & game):
a) Configuration Editor
b) ES Themes
c) Raspi-Config
d) Retropie Setup
...essentially every one I have tried that takes me to one of those blue menu screens the controller has not worked on.

The controller also does not work on the "File Manager" page (which appears to be a different type of interface than the other console menu pages - but I assume is still in LINUX space).

The controller does work on the Retroarch GUI when I launch it from this Retropie menu (just as it works when I am able to access RGUI from other emulators where the hotkey functionality is intact).

Thanks

Hotkey summary sheet