I've just remembered that shortly after purchasing a full SD Card from Technote, one evening after loading the card, the first few folders were missing. It had been working o.k. up to that point so it had to be something I'd done and the suggestion was I had not allowed enough time for the little red light to go out before trying to load a file. This seemed a reasonable explanation to me so this is something else I now watch when loading an SD Card. Needless to say Technote staff kindly put it right for me FREE OF CHARGE and it has been working ever since (touch wood!).
Is it just the one card that misbehaves or all of them? I suspect you are a little wary of trying all your other cards in case the same thing happens again. I'm just curious.
I subscribe to a well known computer magazine and once or twice readers have written in to say they've lost photos off a memory card. Maybe these cards aren't as reliable as the good old floppy albeit they're slow to load. Personally, I'd rather have reliability.