FBA is absolutely a fine emulator, but for NeoGeo games, I stick with gngeo. Maybe is it also because of that superb gui

There is no new version of gngeo-gui, I just released a bugfixed gngeo version, so don't worry about gngeo-gui itself.

About the cause of the crashes in full screen:
for some reason, On Screen Display events triggered a screen resize to 800x480 in full screen mode, which resulted in a segfault.
I just removed a few lines of the code, as this event is totally unneeded on our device. Finding the cause of a crash is mostly the hard part.