The size of the save is determined by what type it is from what I can tell. EEPROM's are 32k and and flash are 256k (or maybe I have that backwards, I can't be bothered to check right now.)
There was an update of the client that broke saves for me. I don't recall which update it was, I think it was one of the ones in which to use the newest loader one had to repatch their games w/ the latest client.
W/ any luck whatever caused them to change how the saves were handled is "fixed" and another "update" won't be needed that breaks saves.