in the info of pnes you can write that if you put the file "disksys.rom" in the pnes folder you can also use famicom disk system file.
add media famicom disk system.
me with rom set 0.2.97.44 and pfbneo 4.3 the neo-geo games work.
try deleting the /switch/pfba folder and putting all the files back (do not overwrite).
thanks for the work you do.
with the set FBA 0.2.97.44 they work well except xenocrisis megadrive.
can you sort them alphabetically when show roms names is selected?