You are talking the difference between advertised shortcuts and non-advertised shortcuts. When you run an application through the repackager and a shortcut is created to an executable that is installed with the application, then the MSI creates an advertised shortcut. If you manually create a shortcut on your dekstop to an app or exe, it is non-advertised.
In short, when an advertised shortcut is clicked on it engages the Windows Installer engine to do a quick check of several key elements of the installation to ensure everything is installed. If something is found to be missing, then Windows Installer initiates a self-repair. This is what you are seeing.
To resolve the issue, you can either edit the resulting package that the repackager creates to make those shortcuts non-advertised, or determine what is causing the self-repair and fix that. Items in the HKCU registry hive or under a user's profile are what typically cause MSI's to initiate a self repair.
