Well, try to remember that the new "Internal" storage you created on the card is now the phones storage. Are you sure it is actually duplicating the apps? Or are you just seeing the names for the apps on the phone and card. Check the actual storage on the phone and on the card.
Also, you could try uninstalling the apps and then downloading them, which put them directly on the card.
Just remember, anything you put on that card now cannot be read by any other device. The SD card is now encoded to that phone.