Ah so desu ka!
I also have the game on the card, and your explanation was worth a lot to me. I HAD noticed that the Palm loads the game from the card each time(please wait...), and keeps the savegame in native storage, but I never followed the dots to realize why I was occasionally losing savegames. Fortunately, I have been using a variation of your backup folder trick, so no great loss, just a frustrating mystery, now solved.