I've released v1.0.9 which fixes the save to cart problem. Best to use and SD2IEC device (or a real disk) to save the save games before updating to v1.0.9, otherwise progress will be lost as the save games are saved as part of the crt file.
But if a new crt file is saved out via the Kung Fu Flash menu (thus including the save games), I can fix it if saving to disk first is not an option .