FBAlpha not reading resolution settings from Retroarch.cfg

[Andrewpk200]

Righto,
So have just got a new enclosure for my pi-arcade and thought now would be a good time to rebuild the system (a long time playing with different settings leaves a lot of mess!)

so i have a new SD card, installed the newest image from here and away i went,
I have all the consoles and games back on but one system is being a pain in the arse!

Anything that i load using FBAlpha is refusing to use the resolution settings from the Config file,

(the main system i am using is the Neogeo folder, but after testing this is affecting games in the Neogeo, FBA & Arcade folders when FBA is the emulator in use)

i have the following in my retroarch.cfg within the Neogeo config folder

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

input_remapping_directory = "/opt/retropie/configs/neogeo/"

video_shader = "/opt/retropie/emulators/retroarch/shader/crt-pi-curvature.glslp"
video_shader_enable = "true"

input_overlay = /opt/retropie/configs/all/consoles-2.cfg
input_overlay_enable = true
input_overlay_opacity = 1.000000
input_overlay_scale = 1.000000

custom_viewport_width = "1280"
custom_viewport_height = "960"
custom_viewport_x = "320"
custom_viewport_y = "60"
aspect_ratio_index = "22"

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

Whenever I launch a game it ignores the resolution parts of the config but does use the Crt-pi shader, it also appears that the game is 'over' the overlay (normally when you get the resolution wrong it disappears behind the overlay.

It does state at the bottom of the screen that the retroarch.cfg has been loaded (this makes sense as it DOES read the shader setting)

any ideas what i am missing here, is there a setting in FBAlpha that overrides these settings, am i doing something really stupid? (Probably, its been a long day)

Pi Model or other hardware: Pi 3
Power Supply used: official 2.5a
RetroPie Version Used 4.3
Built From: 4.3 image from here
USB Devices connected: 1x keyboard + USB harddrive
Controller used: 8BitDo FC30Pro
Error messages received:non
Log found in /dev/shm/runcommand.log (if relevant):
Emulator: FBAlpha

[Andrewpk200]

Well after bashing my head against a desk for an hour or so I finally gave up and posted the above, then figured out almost immediately what the problem was.

Appears at some point within FBA i had set up a core override that must have had resolution settings set up,

Deleted the override file and FBA immediately started behaving itself