Air for IOS: Importing IPA into iTunes

Publishing my app in Flash Builder or Flash Professional works fine and it will import into iTunes the first time. If I create another totally different app, publish it and try and import it into iTunes, I get an alert that says that a version of the application already exists and asks whether I want to replace it. I am not sure if I am doing something wrong, but I should be able to import multiple apps into iTunes without having them replace each other, right? Does anyone have an answer why this is happening? Thanks.