With the default menu mappings B gets mapped to A/OK for MiSTer menus, and A gets mapped to B/back - I would expect this to be the other way around like it is for the SNES controller, as per Nintendo convention.
Should be fixed with the updated mapping that I just pushed. Will you test it (manual download since the updater repo doesn't overwrite existing mappings)?
With the default menu mappings B gets mapped to A/OK for MiSTer menus, and A gets mapped to B/back - I would expect this to be the other way around like it is for the SNES controller, as per Nintendo convention.