That happens to me too. I have since put any new games in the directory, for the fear that I will lose all my current progress. I don't know how to fix it, or why it happens. The only inkling is that I noticed the saved games are named as numbers pertaining to addresses in the fgb browser memory. Adding or deleting a game to the list changes the entire list, and it rewrites the browser memory addresses to new ones, thus making all the savegames void.
I guess its something the author didn't get around to fixing, or just wrote the code that way to get it to work, and then fix it in the future.
DSRAA