I’ve got the .ico file directly in the Files directory. When the shortcut gets created in the Start Menu, though, it doesn’t have the same icon as before… it has the default IE shortcut one. Do custom icons not work for web (.url) shortcuts?
If you reference $dirFiles when creating the shortcut, that folder needs to be present for the lifetime of the shortcut.
If the folder that contains the toolkit is removed after the installation is done, the ico-file is lost and it will not be displayed when viewing the shortcut.