Thanks-something changed and I had to completely rebuild my Ctrlr file. I finally got it to work.
The biggest change was adding multiple keyboard support, and the resulting removing the underscore (_) from the numpad keys (to clarify keyboard number vs numpad number). Wait, from 0.106? Other major changes between the 0.106 and 0.109, IIRC. So rebuilding probably was the quickest way to go.
You noticed what isn't in the ctrlr folder anymore? I didn't think Mame ever had files in that folder.
The official binary comes with four files in the ctrlr folder: hotrod.cfg, hotrodse.cfg, slikstik.cfg, and xarcade.cfg. All are up to date.
MameUI and the mame source do not come with files. Other derivatives may or may not.
All these files have a neogeo section, but there is no neogeo.cfg ctrlr file.