I think the memory card is thing is by system. That is, you need a separate memory card for Japan and US systems. I've heard people save US and Japanese save games on the same card with a freeloader. When I got my Q, it wouldn't read the card that had my Naruto 3 file because the card wasn't formatted for Japanese systems. I had been playing Naruto 3 w/ a Freeloader on my US cube, but even though the file was JPN formatted, the card wasn't. I was also using separate cards for US and JPN save files when using the Freeloader, so even though all the files on the card was JPN formatted, the card itself wasn't.
So I think you need separate cards for when you switch between regions on your Q.