Adam,
You probably used LabVIEW 6.0 before and now you are using version 6.1. There were some changed in the application builder in in version 6.1. The new version uses the MSI installer.
If you create an installer and run it, and you use the same script and create a new installer and run it, you will get the modify/remove/repair dialog. MSI uses a product code to make sure that only one copy of a product is installed at a time. You need to uninstall the first then install the second.
To separate new applications created from an old build script that already has a product code, you can modify the installer by going to the installer properties dialog and generate a new product code.
New Installer Uninstalling Old LabVIEW Built Executable Before Installing Newer VersionRefer to the LabVIEW Application Builder Release Notes (linked below) for a complete list of changes in the Application Builder from LabVIEW 6.0 to 6.1. You also can access the LabVIEW Application Builder Release Notes by selecting Help»Search the LabVIEW Bookshelf.
Product Manuals: LabVIEW Application Builder Release NotesZvezdana S.
National Instruments