This usually happens if you don't change the savegame type to match the one you're trying to open. There should be a dropdown menu in the open file dialog so just change it from PC to Switch and it should let you load it. PC is selected by default which is why it's working for you for those saves.
Since sysbot 1.5, it hasn't played well with cheats. Try holding 'L' as you launch the game and try again. This skips loading the cheats file and may let the poker work.
Location for the configuration file has changed. The path is now /atmosphere/config/system_settings.ini now instead of just /atmosphere/system_settings.ini.