I could never get some NeoGeo games to run thru RA-HEXAECO when booted via WiiFlow. I ended up just popping the ROMS into a different folder and used vanilla RetroArch to boot them.
Thanks for the info. I was hoping this would be a single front end solution, but i guess it's better to just use the stand alone HEXAECO for neogeo games. The Hex neogeo core does work surprisingly great with overlay support.