There's no 'autodiscovery' process running before or outside EmulationStation. The gamelists are written by EmulationStation when stopping/restarting (by default, but you can choose in the option to write it immediately). The location of the gamelists for most of your system (in the games' folder) indicates you either ran a scraper outside of EmulationStation or you copied the games folders from another system (including the system's gamelist.xml). That shouldn't be a problem though.
Did you restart EmulationStation after adding the kidgame tags and before turning on 'kidmode' ? I'm wondering if there isn't any bug that when turning on kid mode doesn't save the metadata on exit (because of the kidmode being selected).
Did you modify the options for metadata saving/reading in EmulationStation ?