Hey Mike,
Instead of putting desktop icons on the "Common Desktop" put them on the "Current user's Desktop".
Also, if the end-user, or the admins for the end-user, screw around with the permissions with the "Current user's Desktop" such that they prevent normal behavior (that is, the current user being able to control the content on the desktop) wyUpdate won't be able to detect it. It will just plow ahead.
Also, you can change how shortcuts are installed in the properties of the wyBuild project (File -> Properties -> General). See "Only add shortcuts if one or more shortcuts previously existed".