You are right. FBNeo is selected as the emulator and there isn't an override set in the gamelist.xml but it is still launching the wrong core.
I decided to move the roms to an usb drive, flash the sd and start again. I did a lot of testing of different options and I may have messed up some configuration somewhere, or corrupted my sd card.
I copied the roms back in and now I'm getting a black screen in FBNeo but I will call that progress, I'm using the emulga romset for NeoGeo but I may need to try a different one set or bios file.
Thanks for making it possible to bring all these amazing games back to life.