The installer for FileUp version 5.4 supports Windows Server 2012. It is highly recommended to upgrade to version 5.4 or higher. (Note: Your application will require additional configuration)
If upgrading is not an option, you can follow the steps in the first part of KB article 1274 for installing FileUp version 5.1.1-5.3.3 without the samples. On Windows 2012, in the "select features" dialog, you also need to uncheck "Documentation."