I have a simple installation which works fine but if I add a shortcut to a web page or an Uninstall shortcut then these are not removed when the package is uninstalled.
I'm not sure why you are encountering this behavior. Is the shortcut still present after the machine is rebooted? If this is the case, please send us the AIP (project) file you are using to support at advancedinstaller dot com so we can investigate it.