Few months (in August to be more exact) ago when I made an update on Wood R4 firmware (in order to play Pokemon Conquest) I had this problem: the old game's saves wouldn't work. I choose a game from Games folder (as always), the games play normally but the saves seem like they don't exist (like I have never played them before). The saves work only after choosing these games from YSMenu. Unfortunately Rune Factory 3 doesn't works through YSMenu and Super Princess Peach freezes when I choose Puzzle option. And when I close the Nintendo DS to trigger its sleep mode it makes weird noises. The only games that don't have problem with saves are games I started after the firmware update.
So my question is: how can I make the saves work again normally by choosing the games from Games folder and not from from YSMenu? I still have the same even after the latest update I made on firmware in October.