From reading stuff on AndroLib, if you go get the Barcode Scanner app, it will work better. When you have both Barcode Scanner and HandyCards installed, and you click the "Add Card by Barcode" option in Handycards, it will ask you if you want to complete the action with Handycards itself or with Barcode Scanner.
This app looks really cool, thanks for posting about it. If I can use it to eliminate these 8 rewards cards from my wallet it will rock. I got it to scan all of them, now I will have to see if the store scanners will pick them up.