fMSX failing to read RETROARCH.CFG properly

[SpudsMcToole]

This is my RETROARCH.CFG for the MSX, located in /opt/retropie/configs/msx as usual.

# Settings made here will only override settings in the global retroarch.cfg if placed above the #include line

#video_shader = "/opt/retropie/emulators/retroarch/shader/barrel-distortion_phosphor.glslp"
#video_shader = "/opt/retropie/emulators/retroarch/shader/arcade-bezel-shader/crt-pi-vertical-curved.glslp"
input_overlay = /opt/retropie/emulators/retroarch/overlays/arcade-bezel-overlays/fergusontx_bare.cfg

input_overlay_scale = 1.400000
input_overlay_opacity = "1.000000"

custom_viewport_width = "1288"
custom_viewport_height = "1080"
custom_viewport_x = "218"
custom_viewport_y = "0"

aspect_ratio_index = "22"

input_remapping_directory = /opt/retropie/configs/msx/

#include "/opt/retropie/configs/all/retroarch.cfg"

BlueMSX runs it fine, adding the overlay and positioning the screen correctly, but fMSX ignores every line about the display EXCEPT the "input_overlay =" one. So I get the overlay, but zoomed right out and with the screen not adjusted to fit it - in other words, a right mess.

"No problem", I thought, "I'll tweak EMULATORS.CFG to tell fMSX to look for a totally different RETROARCH.CFG just for it, with the overlay and screen adjustments disabled."

lr-fmsx = "/opt/retropie/emulators/retroarch/bin/retroarch -L /opt/retropie/libretrocores/lr-fmsx/fmsx_libretro.so --config /opt/retropie/configs/msx/fmsx/retroarch.cfg %ROM%"

But it wasn't having that at all - it just crashed to a black screen, reporting a failure to write to the new RETROARCH.CFG.

(I also tried fixing the settings in the Retroarch menu and then hitting "Save Core Overrides", but it just ignored it.)

Any way round this?