I think your problem is to mix super res and native res. Try "user_mode" (native). I use 25 modes, its enought for me, only native modes, not super. I've tried super for mame, but honestly, can't see any diference.
About FBAneo, I disable "scanlines", set "use low pass filter" for audio and disable "automatically detect fullscreen resulution and aspect ratio. If you do not disable it so fullscreen res will always be 640x480.
About stretch options:
When I set 384x240 cps2 and 320x240 neogeo I set "correct aspect ratio, when I set 384x224 and 304x224 I set "normal stretch"
I don't now why, but fbaneo MVS native res is 304x224 ( groovymame is 320x224) but It looks the same when playing.
So I add 384x224 and 304x224 in "users_modes". and set "arcade" in res options and "normal stretch" in stretch options. When I run cps2 res is 384x224, when I run neogeo MVS res is 304x224 automatically.