retroarch does have an input handler that checks for hotkeys/etc, before it passes your inputs to the emulator, which might add a bit of latency, but it’s pretty simple so i doubt it. you could install retroarch and lr-fba on your PC to see if it’s the same result there?

there’s a couple of other retropie emulators that run neogeo games that might have different results:
lr-mame2003
gngeo
lr-fba-next
(more?)

also, you might get more info at libretro.com/forums as the developers hang out there. let us know what you find :)