Flashram saves randomly getting erased? This is strange...

I experience this problem with the following games: Doubutsu no Mori, Pokémon Snap, Majora's Mask, and Paper Mario. These are all games which use flash memory for saved games. Sometimes it saves correctly, but sometimes when I start up the game, my saved file is completely gone! Sometimes the file is still there, but not from the last time I saved. I am absolutely certain that this does not happen with non-flash games; I played through Banjo-Kazooie and most of Diddy Kong Racing and Super Mario 64 with no save problems. I can always use save states as a workaround, but this still bothers me a little...

"Automatically load a save state"? I've looked through the settings, and I can't find any such option.

The only time I save a state is just before doing a native save, and the only time I load a state is when I find the native save is deleted. Anyway, if save states where the source of the problem, wouldn't it happen with games using other save types too?

Again, I only load a state if the native save is gone. And when I do, saving BEFORE the native save allows me to make a new native save as soon as I load the state save.

I'm quite certain this problem has nothing to do with save states anyway. I only started using save states as a workaround after discovering the saves were getting erased.