Ok, that's unusual- it should be going to whichever virtual card you have in the "slot" at the time.
Try going into the Memory Card Utility in the PS3's Game menu and highlight the card you want to use. Hit the triangle button to bring up a menu along the right side of the screen- you should see an "assign slots" choice in there- hit X on that and tell it slot 1. That should be the card that the game "sees" now.