Right now, the custom app are detected by Product Name and Version which is written to "Programs and Features" after installation. Sometimes we only set some regkeys for modifications or copy files. There is no entry in the programs and features settigns page so we can not detect it if we deploy it as a custom app using PmPC. As a workarond we are currently seetingt some extra keys in the registriy Uninstall path to create a custom product with a version in the installed software list.